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- PDB-3u07: Crystal Structure of the VPA0106 protein from Vibrio parahaemolyt... -

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Basic information

Entry
Database: PDB / ID: 3u07
TitleCrystal Structure of the VPA0106 protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR106.
Componentsuncharacterized protein VPA0106
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / NESG / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Jelly Rolls - #1600 / : / Domain of unknown function DUF1254 / Domain of unknown function DUF1254 superfamily / Protein of unknown function (DUF1254) / Domain of unknown function DUF1214 / Protein of unknown function (DUF1214) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.083 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / 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 VPA0106 protein from Vibrio parahaemolyticus.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein VPA0106
B: uncharacterized protein VPA0106
C: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)153,4523
Polymers153,4523
Non-polymers00
Water14,052780
1
A: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)51,1511
Polymers51,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)51,1511
Polymers51,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: uncharacterized protein VPA0106


Theoretical massNumber of molelcules
Total (without water)51,1511
Polymers51,1511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.445, 96.320, 100.540
Angle α, β, γ (deg.)60.610, 80.870, 86.550
Int Tables number1
Space group name H-MP1
Detailsmonomer,55.15 kD,94.5%

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Components

#1: Protein uncharacterized protein VPA0106


Mass: 51150.629 Da / Num. of mol.: 3 / Mutation: R60E, I64R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA0106 / Plasmid: pET21_NESG, VpR106-RM.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q87JZ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 6
Details: 20% PEG 4000, 0.1M sodium nitrate, 0.1M MES, pH 6.0, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.083→50 Å / Num. all: 198295 / Num. obs: 188380 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 25.05 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 2.8 / Num. unique all: 19654 / % possible all: 79.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.083→46.958 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.6 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 9413 5 %
Rwork0.194 --
obs0.195 188331 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.226 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 124.28 Å2 / Biso mean: 32.622 Å2 / Biso min: 1.71 Å2
Baniso -1Baniso -2Baniso -3
1--5.148 Å20.733 Å20.897 Å2
2--0.266 Å22.341 Å2
3---4.881 Å2
Refinement stepCycle: LAST / Resolution: 2.083→46.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9549 0 0 780 10329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069789
X-RAY DIFFRACTIONf_angle_d1.40313255
X-RAY DIFFRACTIONf_chiral_restr0.1041377
X-RAY DIFFRACTIONf_plane_restr0.0061741
X-RAY DIFFRACTIONf_dihedral_angle_d14.8513633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.083-2.1070.3071620.263356351853
2.107-2.1310.2962490.2554896514577
2.131-2.1570.3062880.2475558584688
2.157-2.1850.2893040.2345997630196
2.185-2.2140.263110.2416034634597
2.214-2.2440.2433000.2226198649897
2.244-2.2760.2243160.2245983629997
2.276-2.310.2423320.2266083641597
2.31-2.3460.2943300.2226152648297
2.346-2.3840.2683490.2145947629697
2.384-2.4250.2443010.2116241654297
2.425-2.470.2593230.2166016633997
2.47-2.5170.2482690.2136079634897
2.517-2.5680.2313690.2216209657897
2.568-2.6240.2553160.2236022633897
2.624-2.6850.2643080.2136179648797
2.685-2.7530.2493070.2146097640497
2.753-2.8270.243440.2096144648898
2.827-2.910.2563040.2116152645697
2.91-3.0040.2563080.2156191649998
3.004-3.1110.2173640.216080644498
3.111-3.2360.2143120.1976190650298
3.236-3.3830.2153320.1936092642498
3.383-3.5610.193060.1856164647098
3.561-3.7840.1953380.1816142648098
3.784-4.0760.1933480.1636167651598
4.076-4.4860.1583360.146163649998
4.486-5.1350.1433500.146170652098
5.135-6.4670.1763110.186165647698
6.467-46.970.2043260.1926051637796
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00210.00010.0030.0016-0.00480.00560.01480.0001-0.019-0.00980.0216-0.00580.01660.011300.06570.0196-0.00190.10620.0815-0.0003-0.2691-0.268-0.2038
20.0018-0.00030.00040.00390.0050.002-0.00270.01830.0074-0.0071-0.0146-0.0169-0.0125-0.0085-00.06610.0046-0.00010.0347-0.10220.07930.058940.612126.7507
30.00120.00410.00080.00550.0012-0.001-0.0039-0.00670.01860.0089-0.01070.00650.00140.00980-0.0018-0.04590.0079-0.04180.02350.0454-0.0887-3.003648.7101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA25 - 435
2X-RAY DIFFRACTION2chain BB25 - 435
3X-RAY DIFFRACTION3chain CC25 - 435

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