+Open data
-Basic information
Entry | Database: PDB / ID: 3e3v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of RecX from Lactobacillus salivarius | ||||||
Components | Regulatory protein recX | ||||||
Keywords | RECOMBINATION / PSI-II / NYSGXRC / RecX / 10123p / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus salivarius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of RecX Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3e3v.cif.gz | 43 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3e3v.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e3v_validation.pdf.gz | 424.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3e3v_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 3e3v_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 3e3v_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3v ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3v | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20597.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus salivarius (bacteria) / Strain: UCC118 / Gene: LSL_0368 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q1WV04 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.49 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2M Ammonium sulfate, 0.1M Na-citrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors |
Radiation | Monochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 10853 / Num. obs: 10853 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 1050 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: None Resolution: 2.04→33.72 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 91775.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0591 Å2 / ksol: 0.377931 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→33.72 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.04→2.17 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|