+Open data
-Basic information
Entry | Database: PDB / ID: 2d40 | ||||||
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Title | Crystal Structure of Z3393 from Escherichia coli O157:H7 | ||||||
Components | putative gentisate 1,2-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Gentisic Acid / 1 / 2-dioxygenase / bicupin / tetramer / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å | ||||||
Authors | Adams, M.A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2006 Title: Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7 Authors: Adams, M.A. / Singh, V.K. / Keller, B.O. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d40.cif.gz | 250.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d40.ent.gz | 205.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d40_validation.pdf.gz | 481.8 KB | Display | wwPDB validaton report |
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Full document | 2d40_full_validation.pdf.gz | 597.5 KB | Display | |
Data in XML | 2d40_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 2d40_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d40 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d40 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40229.637 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: O157:H7 / References: UniProt: Q8X655, gentisate 1,2-dioxygenase #2: Chemical | ChemComp-FE / #3: 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: 1.9 Å3/Da / Density % sol: 36.4 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1M bisTris, 24% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2005 |
Radiation | Monochromator: single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→34.5 Å / Num. all: 44440 / Num. obs: 43818 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.063 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.41→34.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.893 / SU B: 9.054 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.317 / ESU R Free: 0.301 / 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 | Biso mean: 27.271 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→34.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.405→2.467 Å / Total num. of bins used: 20 /
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