+Open data
-Basic information
Entry | Database: PDB / ID: 4fb5 | ||||||
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Title | Crystal structure of a probable oxidoreduxtase protein | ||||||
Components | Probable oxidoreductase protein | ||||||
Keywords | OXIDOREDUCTASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / GFO/IDH/MOCA family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizobium etli (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å | ||||||
Authors | Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a probable oxidoreduxtase protein Authors: Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fb5.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fb5.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fb5_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 4fb5_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 4fb5_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 4fb5_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/4fb5 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fb5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44313.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / ATCC 51251 / Gene: RHE_CH01346 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2KAI6 #2: 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: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.49M Sodium phosphate monobasic, 0.91M Potassium phosphate dibasic, Sarcosine, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 30554 / Num. obs: 30554 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 58.357 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.46 / Num. unique all: 2990 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.471 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.551 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.171 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.611→2.679 Å / Total num. of bins used: 20
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