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- PDB-1gvp: GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) -

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Basic information

Entry
Database: PDB / ID: 1gvp
TitleGENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
ComponentsGENE V PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA REPLICATION
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIERS / Resolution: 1.6 Å
AuthorsSu, S. / Gao, Y.-G. / Zhang, H. / Terwilliger, T.C. / Wang, A.H.-J.
CitationJournal: Protein Sci. / Year: 1997
Title: Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.
Authors: Su, S. / Gao, Y.G. / Zhang, H. / Terwilliger, T.C. / Wang, A.H.
History
DepositionFeb 26, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
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

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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)9,6991
Polymers9,6991
Non-polymers00
Water95553
1
A: GENE V PROTEIN

A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,3982
Polymers19,3982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area11160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.810, 27.920, 42.400
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GENE V PROTEIN


Mass: 9699.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K561 / Gene: GEN V IN BACTERIOPHAGE F1 / Plasmid: PTT2 / Gene (production host): GEN V / Production host: Escherichia coli (E. coli) / Strain (production host): K561 / References: UniProt: P69543
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM SOLUTIONS CONTAINING 10 MG/ML PROTEIN, 4 MM TRIS BUFFER (PH7.5), AND 16% PEG 4000 (W/V), EQUILIBRATED AGAINST 12% PEG 4000 BY VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1994 / Details: COLLIMATORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→8 Å / Num. obs: 9073 / % possible obs: 77.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.6→2 Å / % possible all: 60.8

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISIICdata reduction
R-AXISIIdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIERS / Resolution: 1.6→8 Å / Rfactor Rfree error: 0.0094 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: MEAN B FACTOR INCLUDES THE CONTRIBUTION FROM ALL HYDROGEN ATOMS. THE B-FACTORS OF ALL HYDROGEN ATOMS IN WATER ARE SET TO 35.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 941 10.4 %RANDOM
Rwork0.209 ---
obs0.209 9016 77.9 %-
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.4616 Å20 Å22.8596 Å2
2---0.996 Å20 Å2
3---1.4576 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 0 53 735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.63
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.51.5
X-RAY DIFFRACTIONx_mcangle_it4.152
X-RAY DIFFRACTIONx_scbond_it4.212
X-RAY DIFFRACTIONx_scangle_it6.762.5
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4057 49 9.5 %
Rwork0.3812 468 -
obs--35.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19XM.PROTOPH19X.PRO
X-RAY DIFFRACTION2

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