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Neutron Protein CrystallographyHydrogen, Protons, and Hydration in Bio-macromolecules$

Nobuo Niimura and Alberto Podjarny

Print publication date: 2011

Print ISBN-13: 9780199578863

Published to Oxford Scholarship Online: May 2011

DOI: 10.1093/acprof:oso/9780199578863.001.0001

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(p.206) Appendix B List of bio-macromolecules determined by NPC and deposited in the PDB before May 5, 2010

(p.206) Appendix B List of bio-macromolecules determined by NPC and deposited in the PDB before May 5, 2010

Source:
Neutron Protein Crystallography
Publisher:
Oxford University Press

(p.207)

Proteins

ID

M.W.

Lattice constant

Space group

Resolution

Ref.

Probe

Trypsin Inhibitor

5PTI

6622.57

a = 74.10, b =23.40, c =28.90

P212121

1.0

(1)

N&X

Ribonuclease A

5RSA

13803.37

a = 30.18, b = 38.40, c = 53.32,

P21

2.0

(2)

N&X

β = 105.85

Ribonuclease A

6RSA

14051.54

a = 30.30, b = 38.35, c = 53.70, β = 106.40

P21

2.0

(3)

N&X

Beta-trypsin

1NTP

23467.48

a = 54.84, b = 58.61, c = 67.47

P212121

2.7

(4)

N

Insulin

3INS

11706.08

a = 82.50, c = 34.00

H3

2.2

(5)

N&X

Carbonmonoxymyoglobin

2MB5

18045.70

a = 64.61, b = 30.95, c = 34.86, β = 105.78

P1211

1.8

(6)

N

Triclinic hen egg-white lysozyme

1LZN

14664.22

a = 27.28, b = 32.04, c = 34.27

P1211

1.7

(7)

N

α = 88.8, β = 108.8, γ = 111.6

Myoglobin

1CQ2

17851.60

a = 64.53, b = 30.91, c = 34.78, β = 105.82

P1211

2.0

(8)

N

Concanavalin A

1C57

25717.62

a = 89.11, b = 87.58, c = 63.26

I222

2.4

(9)

N

Hen egg-white lysozyme

1IO5

14331.20

a = 80.80, c = 37.10

P43212

2.0

(10)

N

Endothiapepsin

1GKT

34899.45

a = 43.10, b = 75.70, c = 42.90,

P1211

2.1

(11)

N

β = 97.0

Myoglobin

1L2K

18057.72

a = 64.53, b = 30.87, c = 34.87,

P1211

1.5

(12)

N

β = 105.7

Rubredoxin mutant

1IU6

5919.36

a = 34.48, b = 35.70, c = 43.16

P212121

1.6

(13)

N

Rubredoxin

1VCX

5956.43

a = 34.32, b = 35.31, c = 44.23

P212121

1.5

(14)

N

Concanavalin A

1XQN

25717.62

a = 89.16, b = 86.13, c = 61.59

I222

2.5

(15)

N

Z-DNA hexamer CGCGCG

1V9G

3816.73

a = 18.46, b = 30.76, c = 43.18

P212121

1.8

(16)

N

B-DNA decamer D(CCATTAATGG)2

1WQZ

6088.08

a = 32.90, c = 96.10

P3221

3.0

(17)

N

Protein dsvD

1WQ2

17780.06

a = 60.50, b = 65.10, c = 46.50

P212121

2.4

(18)

N

Immunoglobulin A1 light chain

2ESG

215143.39

N/A

N/A

N/A

(19)

N, Solution

Xylose isomerase

2GVE

43401.57

a = 93.88, b = 99.68, c = 102.90

I222

2.2

(20)

N

Dihydrofolate reductase

2INQ

36951.90

a = 93.12, c = 73.87

P61

2.2

(21)

N

Hemoglobin subunit alpha

2DXM

64547.79

a = 63.79, b = 84.45, c = 54.35, β = 99.33

P1211

2.1

(22)

N

Cubic Insulin

2EFA

5787.66

a = 79.035

I213

2.7

(23)

N

Concanavalin A

2YZ4

25717.62

a = 89.38, b = 87.31, c = 63.05

I222

2.2

(24)

N

Endothiapepsin

2VS2

34636.11

a = 43.03, b = 75.72, c = 42.97, β = 97.02

P21

(25)

D-xylose Isomerase

3CWH

43499.45

a = 94.64, b = 99.97, c = 103.97

I222

2.2

(26)

N

Cubic insulin

2ZPP

5787.66

a = 79.04

I213

2.5

(27)

N

Aldose reductase

2R24

37058.35

a = 50.07, b = 67.13, c = 47.86, β = 92.41

P21

2.19

(28)

N&X

Diisopropyl-fluorophosphatase

3BYC

35201.16

a = 43.44, b = 83.29, c = 87.51

P212121

2.2

(29)

N&X

HIV-1 protease

2ZYE

22149.44

a = 59.5, b = 87.4, c = 46.8

P21212

1.9

(30)

N

Photoactive yellow protein

2ZOI

14052.86

a = 67.15, c = 41.12

P63

1.55

(31)

N

Elastase-1

3HGN

26578.85

a = 50.94, b = 57.46, c = 75.18

P212121

1.2

(32)

N&X

Ribonuclease A

3A1R

13708.40

a = 30.38, b = 38.56, c = 53.4, β = 105.78

P21

1.7

(33)

N

Insulin

3FHP

11706.08

a = 82.85, c = 34.173

H3

2.0

(34)

N

Human lysozyme

2ZWB

14720.80

a = 33.83, b = 56.88, c = 60.97

P212121

*

N

Carbonic anhydrase

3KKY

29354.68

a = 42.6, b = 41.56, c = 72.82

P1211

2.0

(35)

N

2

β = 104.56

Beta-lactamase Toho-1

2WYX

27503.30

a = 72.993, c = 98.365

P3221

2.1

(36)

N

Hemoglobin subunit

3KMF

64547.79

a = 63.79, b = 84.45, c = 54.35

P1211

2.0

(37)

N

alpha

β = 99.33

Amicyanin

3L45

11568.85

a = 27.54, b = 56.58, c = 28.86

P21

1.8&

(38)

N&X

β = 96.21

1.5

Rubredoxin

3KYX

6087.62

a = 34.37, b = 35.34, c = 44.11

P212121

1.68

(39)

N&X

(1.) Wlodawer, A., et al. (1984), Structure of bovine pancreatic trypsin inhibitor: Results of joint neutron and X-ray refinement of crystal form II. J Mol Biol 180 (2): 301–29.

(2.) Wlodawer A., et al. (1986), Comparison of two independently refined models of ribonuclease-A. Acta Cryst B 42 (4): 379–87.

(3.) Borah, B., et al. (1985), Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analog. Biochem 24 (8): 2058–67.

(4.) Kossiakoff, A. (1984), Use of the neutron diffraction–H/D exchange technique to determine the conformational dynamics of trypsin. Basic Life Sci 27: 281–304.

(5.) Wlodawer A., et al. (1989), Structure of insulin: Results of joint neutron and X-ray refinement. Acta Cryst B 45 (1): 99–107.

(6.) Cheng, X. and Schoenborn, B. (1990), Hydration in protein crystals: A neutron diffraction analysis of carbonmonoxymyoglobin. Acta Cryst B 46 (2): 195–208.

(7.) Bon, C., et al. (1999), Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme. Acta Cryst D 55 (5): 978–87.

(8.) Shu, F. et al. (2000), Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin. Proc Natl Acad Sci USA 97 (8): 3872–7.

(9.) Habash, J. et al. (2000), Direct determination of the positions of the deuterium atoms of the bound water in concanavalin A by neutron Laue crystallography. Acta Cryst D Biol Cryst 56(5): 541–50.

(10.) Niimura, N., et al. (1997), Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nat Struct Biol 4 (11): 909–14.

(11.) Coates, L., et al. (2001), A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism. Biochem 40 (44): 13149–57.

(12.) Ostermann, A., et al. (2002), Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 Å resolution. Biophys Chem 95 (3): 183–93.

(13.) Chatake, T., et al. (2004), A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution. Acta Cryst D 60 (8): 1364–73.

(14.) Kurihara, K., et al. (2004), Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules. Proc Natl Acad Sci USA 101 (31): 11215–20.

(15.) Blakeley, M., et al. (2004), The 15-K neutron structure of saccharide-free concanavalin A. Proc Natl Acad Sci USA 101 (47): 16405–10.

(16.) Chatake, T., et al. (2005), The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique. Acta Cryst D Biol Cryst 61 (8): 1088–98.

(17.) Arai, S., et al. (2005), Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements. Nucleic Acids Res 33 (9): 3017–24.

(18.) Chatake, T., et al. (2003), Crystallization and preliminary neutron analysis of the dissimilatory sulfite reductase D (DsrD) protein from the sulfate-reducing bacterium Desulfovibrio vulgaris. Acta Cryst D Biol Cryst 59(12): 2306–9.

(19.) Almogren, A., et al. (2006), Purification, properties and extended solution structure of the complex formed between human immunoglobulin A1 and human serum albumin by scattering and ultracentrifugation. J Mol Biol 356 (2): 413–31.

(20.) Katz, A., et al. (2006), Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction. Proc Natl Acad Sci USA 103 (22): 8342–7.

(21.) Bennett, B., et al. (2006), Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc Natl Acad Sci USA 103 (49): 18493–8.

(22.) Chatake, T., et al. (2007), Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography. J Am Chem Soc 129 (48): 14840–1.

(23.) Ishikawa, T., et al. (2008), A neutron crystallographic analysis of a cubic porcine insulin at pD 6.6. Chem Phys 345 (2–3): 152–8.

(24.) Ahmed, H., et al. (2007), The determination of protonation states in proteins. Acta Cryst D Biol Cryst 63 (8): 906–22.

(25.) Coates, L., et al. (2008), The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction. J Am Chem Soc 130 (23): 7235–7.

(26.) Kovalevsky, A., et al. (2008), Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose. Biochem 47 (29): 7595–7.

(27.) Ishikawa, T., et al. (2008), An abnormal pKa value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis. Biochem Biophys Res Comm 376 (1): 32–5.

(28.) Blakeley, M., et al. (2008), Quantum model of catalysis based on a mobile proton revealed by subatomic X-ray and neutron diffraction studies of h-aldose reductase. Proc Natl Acad Sci USA 105 (6): 1844–8.

(29.) Blum, M., et al. (2009), Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement. Proc Natl Acad Sci USA 106 (3): 713–18.

(30.) Yamaguchi, S., et al. (2009), Low-barrier hydrogen bond in photoactive yellow protein. Proc Natl Acad Sci USA 106 (2): 440–4.

(31.) Adachi, M., et al. (2009), Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography. Proc Natl Acad Sci USA 106 (12): 4641–6.

(32.) Tamada, T., et al. (2009), Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond. J Am Chem Soc 131 (31): 11033–40.

(33.) Yagi, D., et al. (2009), A neutron crystallographic analysis of phosphate-free ribonuclease A at 1.7 Å resolution. Acta Crystallogr D Biol Crystallogr 65 (9): 892–9.

(34.) Iwai, W., et al. (2009), A neutron crystallographic analysis of T6 porcine insulin at 2.1 A resolution. Acta Cryst D Biol Cryst 65 (10): 1042–50.

(35.) Fisher, S., et al. (2010), Neutron structure of human carbonic anhydrase II: Implications for proton transfer. Biochem 49 (3): 415–21.

(36.) Tomanicek, S., et al. (2010), Neutron diffraction studies of a class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant. J Mol Biol 396 (4): 1070–80.

(37.) Kovalevsky, A., et al. (2010), Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the bohr effect. J Mol Biol 398 (2): 276–91.

(38.) Sukumar, N., et al. (2010), A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer. Proc Natl Acad Sci 107 (15): 6817–22.

(39.) Gardberg, A., et al. (2010), Unambiguous determination of H-atom positions: Comparing results from neutron and high-resolution X-ray crystallography. Acta Cryst D 66 (5): 558–67.

(*) to be published.

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