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- PDB-3vb9: Crystal structure of VPA0735 from Vibrio parahaemolyticus in mono... -

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Basic information

Entry
Database: PDB / ID: 3vb9
TitleCrystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109
ComponentsUncharacterized protein VPA0735
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


VPA0735-like fold / VPA0735-like domain / Domain of unknown function DUF1214, C-terminal domain / Domain of unknown function DUF1254 / Domain of unknown function DUF1214, C-terminal domain superfamily / 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) ...VPA0735-like fold / VPA0735-like domain / Domain of unknown function DUF1214, C-terminal domain / Domain of unknown function DUF1254 / Domain of unknown function DUF1214, C-terminal domain superfamily / 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) / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Jelly Rolls / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DUF1254 domain-containing protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeetharaman, J. / Neely, H. / Cunningham, K. / Ciccosanti, C. / Bjelic, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. ...Seetharaman, J. / Neely, H. / Cunningham, K. / Ciccosanti, C. / Bjelic, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of VPA0735 from Vibrio parahaemolyticus in monoclinic form, NorthEast Structural Genomics target VpR109
Authors: Seetharaman, J. / Neely, H. / Cunningham, K. / Ciccosanti, C. / Bjelic, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein VPA0735
B: Uncharacterized protein VPA0735
C: Uncharacterized protein VPA0735
D: Uncharacterized protein VPA0735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,91411
Polymers223,7444
Non-polymers1707
Water15,115839
1
A: Uncharacterized protein VPA0735
B: Uncharacterized protein VPA0735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9696
Polymers111,8722
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-57 kcal/mol
Surface area34490 Å2
MethodPISA
2
C: Uncharacterized protein VPA0735
D: Uncharacterized protein VPA0735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9455
Polymers111,8722
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-71 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.267, 106.929, 157.178
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein VPA0735


Mass: 55935.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VPA0735 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87I71
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7
Details: 200MM MOPS, PEG8000, MGCL2, 10MM DTT, PH 7.0, 0.5M lactose, Microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 237755 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.4
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 4 / % possible all: 79.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P3Y

2p3y


Resolution: 2.1→39.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 59657.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 14075 9.7 %RANDOM
Rwork0.224 ---
obs0.224 118970 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.283 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å20 Å24.042 Å2
2--11.842 Å20 Å2
3----8.862 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14887 0 7 839 15733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006204
X-RAY DIFFRACTIONc_angle_deg1.30103
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.1→2.55 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 2148 10 %
Rwork0.237 19227 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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