+Open data
-Basic information
Entry | Database: PDB / ID: 1og6 | ||||||
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Title | ydhF, an aldo-keto reductase from E.coli complexed with NADPH | ||||||
Components | HYPOTHETICAL OXIDOREDUCTASE YDHF | ||||||
Keywords | OXIDOREDUCTASE / ALDO-KETO REDUCTASE / ALPHA/BETA BARREL / NADPH-DEPENDANT / BACTERIAL TARGETS AT IGS-CNRS / FRANCE / BIGS / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jeudy, S. / Abergel, C. / Claverie, J.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Ydhf, an Aldo-Keto Reductase from Escherichia Coli Authors: Jeudy, S. / Abergel, C. / Claverie, J.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1og6.cif.gz | 184.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1og6.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 1og6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1og6 ftp://data.pdbj.org/pub/pdb/validation_reports/og/1og6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 33648.496 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: THERE IS A RATIO ONE TO ONE PROTEIN MOLECULE AND NADP Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76187 #2: Chemical | #3: 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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | pH: 7 Details: IMIDAZOLE/MALATE 0.2M AMMONIUM SULFATE 0.1M PH7.0, POLY ETHYLENE GLYCOL 16%, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2002 / Details: MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.88 Å / Num. obs: 27329 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 66.8 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1.8 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.91 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 3042373.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FOUR DISORDERED RESIDUES MISSED IN THE CHAIN B
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.409 Å2 / ksol: 0.282 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
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Xplor file |
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