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Yorodumi- PDB-3f5q: CRYSTAL STRUCTURE OF putative short chain dehydrogenase from Esch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f5q | ||||||
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Title | CRYSTAL STRUCTURE OF putative short chain dehydrogenase from Escherichia coli CFT073 | ||||||
Components | dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / dehydrogenase / PSI-2 / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli O6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: to be published Title: Crystal structure of an uncharacterized protein Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f5q.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5q.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 3f5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f5q_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 3f5q_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 3f5q_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 3f5q_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5q ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5q | HTTPS FTP |
-Related structure data
Related structure data | 3eoiC 6iiiC 6inyC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | biological unit is the same as asymmetric unit. |
-Components
#1: Protein | Mass: 29178.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: CFT073 / Gene: AAN80202.1, c1736, yciK / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL References: UniProt: Q8FHV3, UniProt: A0A0H2V6Y9*PLUS, Oxidoreductases #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: 1.98 Å3/Da / Density % sol: 37.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M ammonium acetate, 0.1M HEPES, 25% PEG3350, 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: NSLS / Beamline: X29A / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.8 % / Av σ(I) over netI: 39.86 / Number: 158882 / Rmerge(I) obs: 0.087 / Χ2: 7.8 / D res high: 1.76 Å / D res low: 50 Å / Num. obs: 41952 / % possible obs: 94.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.76→50 Å / Num. obs: 41952 / % possible obs: 94.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Χ2: 7.802 / Net I/σ(I): 39.862 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.75 / FOM acentric: 0.75 / FOM centric: 0 / Reflection: 41211 / Reflection acentric: 41211 / Reflection centric: 0 | |||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.872 / SU B: 4.872 / SU ML: 0.079 / SU R Cruickshank DPI: 0.127 / SU Rfree: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.123 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.7 Å2 / Biso mean: 16.04 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.805 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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