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Yorodumi- PDB-7udd: Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7udd | |||||||||
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Title | Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-trifluoroethanol at 150 K | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase liver NAD 2 / 2 / 2-trifluoroethananol | |||||||||
Function / homology | Function and homology information : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Plapp, B.V. / Gakhar, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2022 Title: Dependence of crystallographic atomic displacement factors on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenases Authors: Plapp, B.V. / Gakhar, L. / Subramanian, R. #1: Journal: Biochemistry / Year: 2012 Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7udd.cif.gz | 347.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7udd.ent.gz | 281.1 KB | Display | PDB format |
PDBx/mmJSON format | 7udd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7udd_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 7udd_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 7udd_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 7udd_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/7udd ftp://data.pdbj.org/pub/pdb/validation_reports/ud/7udd | HTTPS FTP |
-Related structure data
Related structure data | 7ua6SC 7uc9C 7ucaC 7ucuC 7udeC 7udrC 7uecC 7ueeC 7uefC 7ueiC 7uejC 7uhvC 7uhwC 7uhxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/892 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: lover / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 5 types, 887 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MRD / ( #6: Water | ChemComp-HOH / | |
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-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: 2.26 Å3/Da / Density % sol: 45 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL |
-Data collection
Diffraction | Mean temperature: 150 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2009 Details: ROSENBAUM ROCK VERTICAL FOCUSINGMIRROR WITH PT, GLASS, PD LANES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ROSENBAUM ROCK HIGH RESOLUTION DOUBLE CRYSTAL MONOCHROMATOR, LN2 COOLED, SAGITTAL FOCUSSING 2ND MIRROR, SI(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→19.96 Å / Num. obs: 283364 / % possible obs: 94.3 % / Redundancy: 4.01 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.064 / Rsym value: 0.032 / Χ2: 1.19 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ua6 Resolution: 1.1→19.96 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.111 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 68.76 Å2 / Biso mean: 16.35 Å2 / Biso min: 8.5 Å2
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Refinement step | Cycle: final / Resolution: 1.1→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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