[English] 日本語
Yorodumi- PDB-3f6a: Crystal structure of a hydrolase, NUDIX family from Clostridium p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f6a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a hydrolase, NUDIX family from Clostridium perfringens | ||||||
Components | Hydrolase, NUDIX family | ||||||
Keywords | HYDROLASE / NUDIX family / Protein Structure Initiative II(PSI II) / NYSGXRC / 11180h / Structural Genomics / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium perfringens ATCC 13124 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å | ||||||
Authors | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a hydrolase, NUDIX family from Clostridium perfringens Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f6a.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f6a.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f6a ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f6a | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18214.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria) Strain: ATCC 13124/NCTC 8237/ Type A / Gene: CPF_1062 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0TS82, UniProt: A0A0H2YS52*PLUS #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.06 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 0.1M citric acid, 3.0M sodium chloride, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2008 / Details: MIRRORS |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→34.35 Å / Num. all: 21021 / Num. obs: 21021 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1 / Num. unique all: 2033 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.02→34.35 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 95116.3 / 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: 54.304 Å2 / ksol: 0.396111 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→34.35 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|