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Yorodumi- PDB-3dmy: Crystal Structure of a predicated acyl-CoA synthetase from E.coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dmy | ||||||
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Title | Crystal Structure of a predicated acyl-CoA synthetase from E.coli | ||||||
Components | Protein fdrA | ||||||
Keywords | structural genomics / unknown function / Predicted Actyl-CoA synthetase / 10300a / NYSGRC / PSI-II / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / bacterial-type flagellum-dependent cell motility / tricarboxylic acid cycle / membrane => GO:0016020 / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å | ||||||
Authors | Sugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a predicted Acyl-CoA-synthetase from E.coli Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dmy.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dmy.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/3dmy ftp://data.pdbj.org/pub/pdb/validation_reports/dm/3dmy | 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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-Components
#1: Protein | Mass: 51122.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fdrA, ylbD, b0518, JW0506 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47208 #2: 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: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris 6.5, 25% PEG3350, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2008 / Details: mirror |
Radiation | Monochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 66773 / Num. obs: 66773 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2 / % possible all: 64.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.07→48.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 33167.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.3862 Å2 / ksol: 0.329463 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.07→48.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.2 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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