+Open data
-Basic information
Entry | Database: PDB / ID: 1o8c | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH | ||||||
Components | YHDH | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / POSSIBLE NADPH-DEPENDENT QUINONE OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information acrylyl-CoA reductase (NADPH) / acryloyl-CoA reductase (NADPH) activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sulzenbacher, G. / Roig-Zamboni, V. / Pagot, F. / Grisel, S. / Salamoni, A. / Valencia, C. / Bignon, C. / Vincentelli, R. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase Authors: Sulzenbacher, G. / Roig-Zamboni, V. / Pagot, F. / Grisel, S. / Salomoni, A. / Valencia, C. / Campanacci, V. / Vincentelli, R. / Tegoni, M. / Eklund, H. / Cambillau, C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o8c.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o8c.ent.gz | 214.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o8c_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1o8c_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1o8c_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 1o8c_validation.cif.gz | 68.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o8c ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o8c | HTTPS FTP |
-Related structure data
Related structure data | 1o89SC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | TWO COMPLETE DIMERS ARE PRESENT IN THE ASYMMETRIC UNIT,ONE IS FORMED BY CHAINS A,D, THE OTHER BY CHAINS B,C |
-Components
#1: Protein | Mass: 37294.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P26646 #2: Chemical | ChemComp-NDP / #3: Water | ChemComp-HOH / | Compound details | THIS ENTRY IS FROM A STRUCTURAL | Sequence details | RESIDUES -20 TO 0 AND 10 TO 12 MISSING FROM DECK OF COORDINATES. RESIDUES -20 TO 1 ARE FROM THE ...RESIDUES -20 TO 0 AND 10 TO 12 MISSING FROM DECK OF COORDINATE | |
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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: 3.4 Å3/Da / Density % sol: 63 % |
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Crystal grow | pH: 5.5 Details: 8.5 % PEG 8K, 0.1 M NA-ACETATE PH 5.5, 0.01 MM ZNCL2, 5 MM NADPH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43.7 Å / Num. obs: 62012 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE YHD, PDB ID CODE 1O89 Resolution: 2.6→158.11 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.165 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.223 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→158.11 Å
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Refine LS restraints |
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