+Open data
-Basic information
Entry | Database: PDB / ID: 1pc6 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Genomics, NinB | ||||||
Components | Protein ninB | ||||||
Keywords | Structural genomics / unknown function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | NinB fold / NinB / Recombinase NinB / NinB superfamily / NinB protein / Orthogonal Bundle / Mainly Alpha / BETA-MERCAPTOETHANOL / Protein ninB Function and homology information | ||||||
Biological species | Enterobacteria phage lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å | ||||||
Authors | Zhang, R. / Beasley, S. / Maxwell, K.L. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Functional similarities between phage lambda Orf and Escherichia coli RecFOR in initiation of genetic exchange Authors: Maxwell, K.L. / Reed, P. / Zhang, R. / Beasley, S. / Walmsley, A.R. / Curtis, F.A. / Joachimiak, A. / Edwards, A.M. / Sharples, G.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pc6.cif.gz | 61.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pc6.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pc6_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1pc6_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 1pc6_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1pc6_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pc6 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pc6 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer consists of chain A (Mol. A) and chain B (Mol. B). |
-Components
#1: Protein | Mass: 16671.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P03765 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4M Na(AC), Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9797,0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Jul 2, 2002 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 13046 / Num. obs: 12916 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.8 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 29 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1276 / % possible all: 98.4 | ||||||||||||
Reflection | *PLUS Num. measured all: 100809 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.51→36.15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 589846.35 / Data cutoff high rms absF: 589846.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9659 Å2 / ksol: 0.333566 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.5 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→36.15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Software | *PLUS Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 36.2 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|