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Yorodumi- PDB-7bu3: Structure of alcohol dehydrogenase YjgB in complex with NADP from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bu3 | ||||||
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Title | Structure of alcohol dehydrogenase YjgB in complex with NADP from Escherichia coli | ||||||
Components | (Alcohol dehydrogenase) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Alcohol Dehydrogenase | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / fatty acid metabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Nguyen, G.T. / Kim, Y.-G. / Ahn, J.-W. / Chang, J.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Molecules / Year: 2020 Title: Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli . Authors: Nguyen, G.T. / Kim, Y.G. / Ahn, J.W. / Chang, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bu3.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bu3.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bu3_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 7bu3_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 7bu3_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 7bu3_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/7bu3 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/7bu3 | HTTPS FTP |
-Related structure data
Related structure data | 7bu2SC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36146.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Escherichia coli (E. coli) Gene: ahr, AWG90_000500, B9M99_17975, B9T59_09540, C6B13_12130, CDC27_23140, D2188_25420, D3P01_20900, D9G11_20970, D9I87_13335, DND16_13855, DNQ45_13310, DU321_18055, E0L12_15935, ECONIH1_25310, ...Gene: ahr, AWG90_000500, B9M99_17975, B9T59_09540, C6B13_12130, CDC27_23140, D2188_25420, D3P01_20900, D9G11_20970, D9I87_13335, DND16_13855, DNQ45_13310, DU321_18055, E0L12_15935, ECONIH1_25310, ELV08_20515, EQ830_17095, EXX23_18790, EXX53_16635, FNJ83_00500, FV293_01340, MS6198_49940 Production host: Escherichia coli (E. coli) References: UniProt: A0A094VUC2, UniProt: P27250*PLUS, alcohol dehydrogenase (NADP+) |
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#2: Protein | Mass: 36337.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yjgB, ahr, A9P13_23120, A9X72_22295, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_ ...Gene: yjgB, ahr, A9P13_23120, A9X72_22295, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_04570, BvCmsKSP024_01161, BvCmsKSP045_03147, BvCmsKSP067_02166, BvCmsNSP047_01920, CRX46_16815, D9J60_11645, DJ503_08680, DS732_03420, DU309_23350, EC3234A_79c00790, ERS085365_04790, ERS085374_04180, ERS085416_04717, ERS139211_04850, EYY27_20520, FNJ69_20595, NCTC8959_04532, NCTC9050_02355, NCTC9077_05531, NCTC9117_05474, PGD_03453, SAMEA3472056_04737, WR15_06500, YDC107_2991 Production host: Escherichia coli (E. coli) References: UniProt: A0A024L8S1, UniProt: P27250*PLUS, alcohol dehydrogenase (NADP+) |
-Non-polymers , 6 types, 602 molecules
#3: Chemical | ChemComp-ASP / | ||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, pH 7.0, 16% (w/v) PEG 3350 , 0.2 M Lithium Sulfate, 5 mM NADPH |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→29.55 Å / Num. obs: 134685 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 8.07 |
Reflection shell | Resolution: 1.45→1.49 Å / Num. unique obs: 9859 / CC1/2: 0.038 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7BU2 Resolution: 2→29.55 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.55 Å
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Refine LS restraints |
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LS refinement shell |
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