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Yorodumi- PDB-1gkh: MUTANT K69H OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gkh | ||||||
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Title | MUTANT K69H OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) | ||||||
Components | GENE V PROTEIN | ||||||
Keywords | DNA 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIERS / Resolution: 1.7 Å | ||||||
Authors | Su, S. / Gao, Y.-G. / Zhang, H. / Terwilliger, T.C. / Wang, A.H.-J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gkh.cif.gz | 34.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gkh.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gkh_validation.pdf.gz | 411 KB | Display | wwPDB validaton report |
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Full document | 1gkh_full_validation.pdf.gz | 412.3 KB | Display | |
Data in XML | 1gkh_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1gkh_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gkh ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gkh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | |||||||||||||||||||||||||
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Crystal grow | Method: 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
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1994 / Details: COLLIMATORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.7→1.78 Å / % possible all: 58.8 |
Reflection shell | *PLUS % possible obs: 58.8 % |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 36.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3605 |