+Open data
-Basic information
Entry | Database: PDB / ID: 2c91 | ||||||
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Title | mouse succinic semialdehyde reductase, AKR7A5 | ||||||
Components | AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2 | ||||||
Keywords | OXIDOREDUCTASE / ALDO/KETO REDUCTASE / AKR / SUCCINIC SEMIALDEHYDE REDUCTASE / TARTRATE / GOLGI STACK / NAD / NADP | ||||||
Function / homology | Function and homology information phenanthrene-9,10-epoxide hydrolase activity / : / Aflatoxin activation and detoxification / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / nuclear envelope / Golgi apparatus / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhu, X. / Ellis, E.M. / Lapthorn, A.J. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Crystal Structure of Mouse Succinic Semialdehyde Reductase Akr7A5: Structural Basis for Substrate Specificity. Authors: Zhu, X. / Lapthorn, A.J. / Ellis, E.M. #1: Journal: FEBS Lett. / Year: 2002 Title: Characterisation of a Novel Mouse Liver Aldo-Keto Reductase Akr7A5 Authors: Hinshelwood, A. / Mcgarvie, G. / Ellis, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" 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 "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 | 2c91.cif.gz | 685 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c91.ent.gz | 571 KB | Display | PDB format |
PDBx/mmJSON format | 2c91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c91 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c91 | HTTPS FTP |
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-Related structure data
Related structure data | 1gveS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 37667.613 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: LIVER / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q8CG76, Oxidoreductases |
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-Non-polymers , 6 types, 2161 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-TLA / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-MES / #7: 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: 3.03 Å3/Da / Density % sol: 59.4 % Description: STATISTICS ARE GOOD TO 2.5A RESOLUTION RMERGE 0.43 IN FINAL SHELL. HOWEVER WEEK DATA EXTENDS TO 2.3A RESOLUTION AND WAS INCLUDED IN THE REFINEMENT. |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: SITTING DROP METHOD EQUILIBRATION OF 15 MG/ML AKR7A5, 20MM TRIS-CL PH7.5, 0.5M DITHITHREITOL, 1MM NADP AGAINST 0.2M SODIUM TARTRATE, 7.5% PEG8000 AND 0.1M MES-NAOH PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 24, 2003 / Details: RH COATED SI MIRROR |
Radiation | Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42 Å / Num. obs: 630867 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GVE, CHAIN A Resolution: 2.3→45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.094 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.196 / Stereochemistry target values: MAWIMUM 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 mean: 33.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45 Å
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Refine LS restraints |
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