+Open data
-Basic information
Entry | Database: PDB / ID: 1gvp | ||||||
---|---|---|---|---|---|---|---|
Title | GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) | ||||||
Components | GENE V PROTEIN | ||||||
Keywords | DNA 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIERS / Resolution: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gvp.cif.gz | 34.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gvp.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gvp_validation.pdf.gz | 412.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gvp_full_validation.pdf.gz | 414.5 KB | Display | |
Data in XML | 1gvp_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1gvp_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gvp ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gvp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
---|---|
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 |
-Data collection
Diffraction | Mean temperature: 285 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 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: 1.6→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 shell | Resolution: 1.6→2 Å / % possible all: 60.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|