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Yorodumi- PDB-3isa: CRYSTAL STRUCTURE OF putative enoyl-CoA hydratase/isomerase FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3isa | ||||||
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Title | CRYSTAL STRUCTURE OF putative enoyl-CoA hydratase/isomerase FROM Bordetella parapertussis | ||||||
Components | Putative enoyl-CoA hydratase/isomerase | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / enoyl-CoA hydratase / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / Isomerase | ||||||
Function / homology | Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / isomerase activity / Alpha-Beta Complex / Alpha Beta / Putative enoyl-CoA hydratase/isomerase Function and homology information | ||||||
Biological species | Bordetella parapertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Patskovsky, Y. / Malashkevich, V. / Toro, R. / Foti, R. / Dickey, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF enoyl-CoA hydratase FROM Bordetella parapertussis Authors: Patskovsky, Y. / Malashkevich, V. / Toro, R. / Foti, R. / Dickey, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3isa.cif.gz | 334.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3isa.ent.gz | 269.9 KB | Display | PDB format |
PDBx/mmJSON format | 3isa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/3isa ftp://data.pdbj.org/pub/pdb/validation_reports/is/3isa | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 27627.350 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: BPP4107 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7W3D6 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / #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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 1.5M SODIUM CHLORIDE, PH 7.5, 10% ETHANOL, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 175921 / % possible obs: 97.3 % / Observed criterion σ(I): -5 / Redundancy: 2.1 % / Biso Wilson estimate: 24.855 Å2 / Rsym value: 0.077 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 0.6 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.552 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.105 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1748 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.761→1.806 Å / Total num. of bins used: 20
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