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Yorodumi- PDB-4ep8: Initial Urease Structure for Radiation Damage Experiment at 100 K -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ep8 | ||||||
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Title | Initial Urease Structure for Radiation Damage Experiment at 100 K | ||||||
Components |
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Keywords | HYDROLASE / alpha-beta barrel / nickel metalloenzyme / radiation damage | ||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | Enterobacter aerogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Warkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Spatial distribution of radiation damage to crystalline proteins at 25-300 K. Authors: Warkentin, M. / Badeau, R. / Hopkins, J.B. / Thorne, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ep8.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ep8.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ep8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/4ep8 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/4ep8 | HTTPS FTP |
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-Related structure data
Related structure data | 4ek0C 4ekaC 4ekbC 4ekhC 4ekoC 4ektC 4el2C 4el3C 4el7C 4elaC 4epbC 4epdC 4epeC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60278.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ureC / Production host: Escherichia coli (E. coli) / References: UniProt: P18314, urease | ||
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#2: Protein | Mass: 11125.690 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ureB / Production host: Escherichia coli (E. coli) / References: UniProt: P18315, urease | ||
#3: Protein | Mass: 11100.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter aerogenes (bacteria) / Gene: ureA / Production host: Escherichia coli (E. coli) / References: UniProt: P18316, urease | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: lithium sulfate, hepes, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 24, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. obs: 114735 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.042 / Χ2: 1.431 / Net I/σ(I): 18.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→15.62 Å / Cor.coef. Fo:Fc: 0.9696 / Cor.coef. Fo:Fc free: 0.9628 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 98.8 Å2 / Biso mean: 23.7655 Å2 / Biso min: 11.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.182 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→15.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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