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Yorodumi- PDB-2bp1: Structure of the aflatoxin aldehyde reductase in complex with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bp1 | ||||||
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Title | Structure of the aflatoxin aldehyde reductase in complex with NADPH | ||||||
Components | AFLATOXIN B1 ALDEHYDE REDUCTASE MEMBER 2 | ||||||
Keywords | OXIDOREDUCTASE / ALDO-KETO REDUCTASE FAMILY 7 / SSA REDUCTASE / TIM BARREL | ||||||
Function / homology | Function and homology information phenanthrene-9,10-epoxide hydrolase activity / : / aldehyde metabolic process / Aflatoxin activation and detoxification / aldo-keto reductase (NADPH) activity / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / lipid metabolic process / carbohydrate metabolic process ...phenanthrene-9,10-epoxide hydrolase activity / : / aldehyde metabolic process / Aflatoxin activation and detoxification / aldo-keto reductase (NADPH) activity / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / lipid metabolic process / carbohydrate metabolic process / electron transfer activity / Golgi apparatus / mitochondrion / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Debreczeni, J.E. / Lukacik, P. / Kavanagh, K. / Dubinina, E. / Bray, J. / Colebrook, S. / Haroniti, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. ...Debreczeni, J.E. / Lukacik, P. / Kavanagh, K. / Dubinina, E. / Bray, J. / Colebrook, S. / Haroniti, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Gileadi, O. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Structure of the Aflatoxin Aldehyde Reductase in Complex with Nadph Authors: Debreczeni, J.E. / Lukacik, P. / Kavanagh, K. / Dubinina, E. / Bray, J. / Colebrook, S. / Haroniti, A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / Gileadi, O. / Oppermann, U. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA", "DA" IN EACH CHAIN ON ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA", "DA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 2bp1.cif.gz | 272 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bp1.ent.gz | 219.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bp1_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2bp1_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2bp1_validation.xml.gz | 52.7 KB | Display | |
Data in CIF | 2bp1_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bp1 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bp1 | HTTPS FTP |
-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: Ens-ID: 1 / Refine code: 2
NCS oper:
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-Components
#1: Protein | Mass: 39725.000 Da / Num. of mol.: 4 / Fragment: RESIDUES 30-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: O43488 #2: Chemical | ChemComp-NDP / #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: 2.25 Å3/Da / Density % sol: 45 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: SITTING DROP RESERVOIR: 0.2 M AMMONIUM CITRATE 20 % PEG3350 PROTEIN: 0.01 M HEPES PH 7.5 0.5 M NACL 5 % GLYCEROL 0.5 % TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.912 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 13, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.912 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.98 Å / Num. obs: 49989 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 1.62 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.9 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GVE Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.093 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.244 / 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 mean: 28.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40 Å
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Refine LS restraints |
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