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Yorodumi- PDB-4aub: the complex Structure of the bacterial aldo-keto reductase AKR14A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aub | ||||||
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Title | the complex Structure of the bacterial aldo-keto reductase AKR14A1 with NADP and citrate | ||||||
Components | ALDO-KETO REDUCTASE AKR14A1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information methylglyoxal catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / DNA damage response Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Zhu, X. / Ellis, E.M. / Lapthorn, A. | ||||||
Citation | Journal: Chem.Biol.Interact / Year: 2013 Title: The Diversity of Microbial Aldo/Keto Reductases from Escherichia Coli K12. Authors: Lapthorn, A.J. / Zhu, X. / Ellis, E.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 "BB" 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. THE SHEETS PRESENTED AS "DB" 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 "EB" 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 "FB" 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 "GB" 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 "HB" 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 | 4aub.cif.gz | 526.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aub.ent.gz | 431.6 KB | Display | PDB format |
PDBx/mmJSON format | 4aub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aub_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4aub_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4aub_validation.xml.gz | 104.8 KB | Display | |
Data in CIF | 4aub_validation.cif.gz | 142.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4aub ftp://data.pdbj.org/pub/pdb/validation_reports/au/4aub | HTTPS FTP |
-Related structure data
Related structure data | 4astC 1exbS C: citing same article (ref.) S: Starting model for refinement |
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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: 41047.453 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q46851 #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-FLC / #4: 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: 2.68 Å3/Da / Density % sol: 54.2 % Description: STATISTICS ARE GOOD TO 2.21 ANGSTROM RESOLUTION, RMERGE 0.48 IN FINAL SHELL. HOWEVER THE WEAK REFLECTION EXTENDS TO 2.05 ANGSTROM RESOLUTION AND WAS INCLUDED IN REFINEMENT |
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Crystal grow | pH: 5.4 Details: 0.1M CITRATE BUFFER (PH 5.4), 18% W/V PEG 2000 MME AND 0.2 M AMMONIUM SULPHATE SUPPLEMENTED WITH 1 MM NADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→48.8 Å / Num. obs: 194971 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.8 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EXB Resolution: 2.05→95.35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.57 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.179 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.481 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→95.35 Å
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