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- PDB-3c0d: Crystal structure of the putative nitrite reductase NADPH (small ... -

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Basic information

Entry
Database: PDB / ID: 3c0d
TitleCrystal structure of the putative nitrite reductase NADPH (small subunit) oxidoreductase protein Q87HB1. Northeast Structural Genomics Consortium target VpR162
ComponentsPutative nitrite reductase NADPH (Small subunit) oxidoreductase protein
KeywordsOXIDOREDUCTASE / NESG / VpR162 / Q87HB1 / XRAY / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


nitrite reductase [NAD(P)H] activity / nitrate assimilation / 2 iron, 2 sulfur cluster binding
Similarity search - Function
Rieske-like [2Fe-2S] domain, NirD-type / Nitrite reductase (NADH) small subunit / Rieske-like [2Fe-2S] domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKuzin, A.P. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, D. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, D. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the putative nitrite reductase NADPH (small subunit) oxidoreductase protein Q87HB1.
Authors: Kuzin, A.P. / Abashidze, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, D. / Fang, Y. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJan 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
B: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
C: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
D: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
E: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
F: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
G: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein
H: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)108,9368
Polymers108,9368
Non-polymers00
Water1,42379
1
A: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Theoretical massNumber of molelcules
Total (without water)13,6171
Polymers13,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.667, 103.462, 82.951
Angle α, β, γ (deg.)90.00, 91.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative nitrite reductase NADPH (Small subunit) oxidoreductase protein


Mass: 13617.009 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA1054 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87HB1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 1, 2007 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 78585 / Num. obs: 78585 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2.892 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.044 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.216 / Rsym value: 0.314 / % possible all: 84

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Processing

Software
NameVersionClassification
CNS1.2refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 331560.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. BULK SOLVENT MODEL WAS USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2935 5 %RANDOM
Rwork0.241 ---
obs0.241 59074 73.8 %-
all-70404 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.6997 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1--14.18 Å20 Å2-3.23 Å2
2--31.18 Å20 Å2
3----17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6651 0 0 79 6730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.654
X-RAY DIFFRACTIONc_mcangle_it2.929
X-RAY DIFFRACTIONc_scbond_it2.215
X-RAY DIFFRACTIONc_scangle_it3.218
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 253 4.2 %
Rwork0.378 5785 -
obs--45.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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