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- PDB-1gkh: MUTANT K69H OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) -

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Basic information

Entry
Database: PDB / ID: 1gkh
TitleMUTANT K69H OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
ComponentsGENE V PROTEIN
KeywordsDNA BINDING PROTEIN / MUTANT / K69H / GVP / SINGLE-STRANDED DNA-BINDING PROTEIN / DNA-BINDING PROTEIN
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: 1.7 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
DepositionMar 4, 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 1.3Nov 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 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,7081
Polymers9,7081
Non-polymers00
Water90150
1
A: GENE V PROTEIN

A: GENE V PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,4162
Polymers19,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1810 Å2
ΔGint-21 kcal/mol
Surface area10860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.660, 27.750, 41.790
Angle α, β, γ (deg.)90.00, 102.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GENE V PROTEIN


Mass: 9708.181 Da / Num. of mol.: 1 / Mutation: K69H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GEN V IN BACTERIOPHAGE F1 / Plasmid: PTT18 / Gene (production host): GEN V IN BACTERIOPHAGE F1 / 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.: 50 / 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
Temp details: room temp
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
24 mMTris-HCl1drop
316 %(w/v)PEG40001drop
412 %(w/v)PEG40001reservoir

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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: Jan 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: 1.7→15 Å / Num. obs: 7813 / % possible obs: 81.38 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.78 Å / % possible all: 58.8
Reflection shell
*PLUS
% possible obs: 58.8 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
R-AXISIICdata reduction
R-AXISIIdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIERS / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.312 829 10.6 %RANDOM
Rwork0.217 ---
obs0.217 7813 81.4 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.6917 Å20 Å25.5535 Å2
2---1.6457 Å20 Å2
3---0.954 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 0 50 723
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_deg3.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.571.5
X-RAY DIFFRACTIONx_mcangle_it5.462
X-RAY DIFFRACTIONx_scbond_it5.292
X-RAY DIFFRACTIONx_scangle_it7.882.5
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3354 81 11.6 %
Rwork0.3605 617 -
obs--58.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19XM.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58
LS refinement shell
*PLUS
Rfactor obs: 0.3605

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