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- PDB-1vqj: GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 (V35I) -

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Basic information

Entry
Database: PDB / ID: 1vqj
TitleGENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 (V35I)
ComponentsGENE V PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / MUTANT / GENE V / BACTERIOPHAGE
Function / homology
Function and homology information


rolling circle single-stranded viral DNA replication / single-stranded DNA binding / DNA replication
Similarity search - Function
Bacteriophage M13, G5P, DNA-binding / Helix-destabilising protein / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-Binding protein G5P
Similarity search - Component
Biological speciesEnterobacteria phage f1 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsZhang, H. / Skinner, M.M. / Sandberg, W.S. / Wang, A.H.-J. / Terwilliger, T.C.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Context dependence of mutational effects in a protein: the crystal structures of the V35I, I47V and V35I/I47V gene V protein core mutants.
Authors: Zhang, H. / Skinner, M.M. / Sandberg, W.S. / Wang, A.H. / Terwilliger, T.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Difference Refinement: Obtaining Differences between Two Related Structures
Authors: Terwilliger, T.C. / Berendzen, J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of the Gene V Protein of Bacteriophage F1 Determined by Multiwavelength X-Ray Diffraction on the Selenomethionyl Protein
Authors: Skinner, M.M. / Zhang, H. / Leschnitzer, D.H. / Guan, Y. / Bellamy, H. / Sweet, R.M. / Gray, C.W. / Konings, R.N. / Wang, A.H. / Terwilliger, T.C.
History
DepositionAug 14, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_keywords / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,7131
Polymers9,7131
Non-polymers00
Water81145
1
A: GENE V PROTEIN

A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,4262
Polymers19,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)76.140, 28.110, 42.560
Angle α, β, γ (deg.)90.00, 103.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GENE V PROTEIN / GVP / G5P / V35I


Mass: 9713.241 Da / Num. of mol.: 1 / Mutation: V35I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage f1 (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P69543
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMprotein1drop
210 mMTris-HCl1drop
315 %(w/v)PEG34001drop
412 %PEG34001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8055 / % possible obs: 97.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.047
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 26381

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MAR600data reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→5 Å / σ(F): 2
Details: SIDE CHAIN DISORDERED DENSITY FOR GLN 12 IS MODELED STEREOCHEMICALLY.
RfactorNum. reflection
Rwork0.206 -
obs0.206 7437
Displacement parametersBiso mean: 20 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 0 45 858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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