[English] 日本語
Yorodumi- PDB-4rd7: The crystal structure of a Cupin 2 conserved barrel domain protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rd7 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a Cupin 2 conserved barrel domain protein from Salinispora arenicola CNS-205 | ||||||
Components | Cupin 2 conserved barrel domain protein | ||||||
Keywords | UNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro | ||||||
Function / homology | Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Cupin 2 conserved barrel domain protein Function and homology information | ||||||
Biological species | Salinispora arenicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.571 Å | ||||||
Authors | Tan, K. / Gu, M. / Clancy, S. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a Cupin 2 conserved barrel domain protein from Salinispora arenicola CNS-205 Authors: Tan, K. / Gu, M. / Clancy, S. / Phillips Jr., G.N. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rd7.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rd7.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 4rd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rd7 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rd7 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14571.407 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salinispora arenicola (bacteria) / Strain: CNS-205 / Gene: Sare_2150 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pGrow7-K / References: UniProt: A8M0K5 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.43 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1.6M Ammonium Sulfate, 0.1M MES:NaOH, 10% (v/v) Dioxane, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2014 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→36.5 Å / Num. all: 18841 / Num. obs: 18841 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 14 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 47.2 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.9 / Num. unique all: 891 / % possible all: 99.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.571→36.497 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 18.81 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.571→36.497 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|