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Yorodumi- PDB-3f5s: CRYSTAL STRUCTURE OF putatitve short chain dehydrogenase from Shi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f5s | ||||||
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Title | CRYSTAL STRUCTURE OF putatitve short chain dehydrogenase from Shigella flexneri 2a str. 301 | ||||||
Components | dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / dehydrogenase / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.36 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 putatitve short chain dehydrogenase from Shigella flexneri 2a str. 301 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 | 3f5s.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5s.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f5s_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 3f5s_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 3f5s_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3f5s_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5s ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5s | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28363.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a str. 301 / Gene: AAP16771.1, S1358, SF1273, yciK / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q83RM3, UniProt: A0A0H2UYY2*PLUS #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: 37.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.1M tris-hcl, 0.2 sodium acetate, pH 8.5, 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: 3.5 % / Av σ(I) over netI: 25.92 / Number: 652231 / Rmerge(I) obs: 0.064 / Χ2: 1.58 / D res high: 1.34 Å / D res low: 50 Å / Num. obs: 184342 / % possible obs: 94.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.34→50 Å / Num. obs: 184342 / % possible obs: 94.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.583 / Net I/σ(I): 25.921 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing dm | FOM : 0.66 / FOM acentric: 0.67 / FOM centric: 0.57 / Reflection: 92307 / Reflection acentric: 90023 / Reflection centric: 2284 | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm shell |
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-Processing
Software |
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Refinement | Resolution: 1.36→7.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.884 / SU B: 1.679 / SU ML: 0.034 / SU R Cruickshank DPI: 0.06 / SU Rfree: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.062 / 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: 500 Å2 / Biso mean: 15.753 Å2 / Biso min: 4.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.394 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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