[English] 日本語
Yorodumi- PDB-3o1q: Native Crystal Structure of Helicobacter pylori Urease Accessory ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o1q | ||||||
---|---|---|---|---|---|---|---|
Title | Native Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF | ||||||
Components | Urease accessory protein ureF | ||||||
Keywords | METAL BINDING PROTEIN / urease maturation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Fong, Y.H. / Chen, Y.W. / Wong, K.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Assembly of Preactivation Complex for Urease Maturation in Helicobacter pylori: CRYSTAL STRUCTURE OF UreF-UreH PROTEIN COMPLEX. Authors: Fong, Y.H. / Wong, H.C. / Chuck, C.P. / Chen, Y.W. / Sun, H. / Wong, K.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3o1q.cif.gz | 147.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3o1q.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o1q_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3o1q_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 3o1q_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3o1q_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/3o1q ftp://data.pdbj.org/pub/pdb/validation_reports/o1/3o1q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28651.834 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureF, HP_0069 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09065 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.97 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Bis-Tris pH 7.0 and 28% PEG MME 5000 , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | |||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2010 | |||||||||||||||||||||
Radiation | Monochromator: rigkau varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.85→50.95 Å / Num. all: 68238 / Num. obs: 68238 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.225 Å / SU ML: 0.23 / σ(F): 1.38 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.79 Å2 / ksol: 0.395 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→40.225 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|