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Yorodumi- PDB-3gkb: Crystal structure of a putative enoyl-CoA hydratase from Streptom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gkb | ||||||
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Title | Crystal structure of a putative enoyl-CoA hydratase from Streptomyces avermitilis | ||||||
Components | Putative enoyl-CoA hydratase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
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 / catalytic activity / Alpha-Beta Complex / Alpha Beta / Putative enoyl-CoA hydratase Function and homology information | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Bonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Romero, R. / Wasserman, 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 a putative enoyl-CoA hydratase from Streptomyces avermitilis Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Chang, S. / Romero, R. / Wasserman, 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 | 3gkb.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gkb.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gkb_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 3gkb_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 3gkb_validation.xml.gz | 36 KB | Display | |
Data in CIF | 3gkb_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/3gkb ftp://data.pdbj.org/pub/pdb/validation_reports/gk/3gkb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION. |
-Components
#1: Protein | Mass: 30539.457 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: echA1, SAV492, SAV_492 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q82QL3 #2: Chemical | #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: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5 Details: 100mM Sodium acetate pH 5.0, 33% PEG 4000, 200mM Ammonium acetate, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 4, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→77.224 Å / Num. all: 74987 / Num. obs: 74217 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 5.6 / Num. unique all: 10730 / Rsym value: 0.259 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.473 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.852 / SU B: 2.314 / SU ML: 0.073 / SU R Cruickshank DPI: 0.125 / SU Rfree: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.118 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.27 Å2 / Biso mean: 20.445 Å2 / Biso min: 8.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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