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- PDB-3nlc: Crystal structure of the VP0956 protein from Vibrio parahaemolyti... -

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Basic information

Entry
Database: PDB / ID: 3nlc
TitleCrystal structure of the VP0956 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR147
ComponentsUncharacterized protein VP0956
KeywordsStructural Genomics / Unknown function / FAD-binding protein / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Alpha-Beta Plaits - #2700 / FAD dependent protein / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the VP0956 protein from Vibrio parahaemolyticus.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, D. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein VP0956
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6632
Polymers60,8771
Non-polymers7861
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.079, 78.166, 101.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein VP0956


Mass: 60877.148 Da / Num. of mol.: 1 / Mutation: G235D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP0956 / Plasmid: VpR147-14.4-ss / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +magic / References: UniProt: Q87R42
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 9
Details: 20% PEG 4000, 0.1M magnesium sulfate, 0.001M FAD, 0.1M TAPS, pH 9.0, microbatch under Paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 57928 / Num. obs: 57001 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 34.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 4.9 / Num. unique all: 5796 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.15→36.49 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.92 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 2868 5.04 %RANDOM
Rwork0.2153 ---
obs0.2182 56907 98.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.271 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4844 Å20 Å2-0 Å2
2--13.4429 Å2-0 Å2
3----3.9585 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 53 112 4225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094202
X-RAY DIFFRACTIONf_angle_d1.215691
X-RAY DIFFRACTIONf_dihedral_angle_d18.9161564
X-RAY DIFFRACTIONf_chiral_restr0.08622
X-RAY DIFFRACTIONf_plane_restr0.006745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1502-2.18720.36721110.30912671X-RAY DIFFRACTION97
2.1872-2.2270.37571490.26772769X-RAY DIFFRACTION100
2.227-2.26980.33951710.25162737X-RAY DIFFRACTION100
2.2698-2.31620.27021300.24932772X-RAY DIFFRACTION100
2.3162-2.36650.31481510.23282754X-RAY DIFFRACTION100
2.3665-2.42150.30811640.23692701X-RAY DIFFRACTION100
2.4215-2.48210.34321570.25322752X-RAY DIFFRACTION100
2.4821-2.54920.35121380.26732756X-RAY DIFFRACTION100
2.5492-2.62420.36321410.26812734X-RAY DIFFRACTION100
2.6242-2.70880.29851430.26142724X-RAY DIFFRACTION100
2.7088-2.80560.29981570.24822763X-RAY DIFFRACTION100
2.8056-2.91790.32161370.22662746X-RAY DIFFRACTION100
2.9179-3.05070.2871500.22842746X-RAY DIFFRACTION100
3.0507-3.21140.28381430.22772734X-RAY DIFFRACTION100
3.2114-3.41250.28031110.21672781X-RAY DIFFRACTION99
3.4125-3.67570.26311470.21222676X-RAY DIFFRACTION98
3.6757-4.04520.23281500.19862669X-RAY DIFFRACTION97
4.0452-4.62950.22791430.15632602X-RAY DIFFRACTION94
4.6295-5.82890.20621490.16132591X-RAY DIFFRACTION95
5.8289-36.49510.20421260.17822361X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: 23.9254 Å / Origin y: 30.9003 Å / Origin z: 65.1736 Å
111213212223313233
T0.2091 Å20.0253 Å2-0.025 Å2-0.2195 Å2-0.0441 Å2--0.1734 Å2
L0.4672 °20.0369 °2-0.0924 °2-0.576 °20.1644 °2--0.1039 °2
S-0.0362 Å °0.152 Å °-0.0625 Å °0.0649 Å °0.0001 Å °0.0356 Å °-0.0322 Å °0.0167 Å °0 Å °
Refinement TLS groupSelection details: chain A

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