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Yorodumi- PDB-3sf5: Crystal Structure of Helicobacter pylori Urease Accessory Protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sf5 | ||||||
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Title | Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H complex | ||||||
Components | (Urease accessory protein ...) x 2 | ||||||
Keywords | CHAPERONE / Urease Accessory Protein / UreF / UreH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.495 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sf5.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sf5.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 3sf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sf5_validation.pdf.gz | 493.8 KB | Display | wwPDB validaton report |
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Full document | 3sf5_full_validation.pdf.gz | 505.4 KB | Display | |
Data in XML | 3sf5_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 3sf5_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/3sf5 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/3sf5 | HTTPS FTP |
-Related structure data
Related structure data | 3o1qSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
-Urease accessory protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 28651.834 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureF / Production host: Escherichia coli (E. coli) / References: UniProt: Q09065 #2: Protein | Mass: 29757.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: ureH / Production host: Escherichia coli (E. coli) / References: UniProt: Q09067 |
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-Non-polymers , 4 types, 223 molecules
#3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16% PEG 4000, 0.15M ammonium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 21, 2010 | ||||||||||||
Radiation | Monochromator: Ni MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2.495→50 Å / Num. all: 36735 / Num. obs: 36388 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 29.96 Å2 | ||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O1Q Resolution: 2.495→35.827 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8702 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 19.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.069 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.54 Å2 / Biso mean: 31.7302 Å2 / Biso min: 8.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.495→35.827 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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