+Open data
-Basic information
Entry | Database: PDB / ID: 1q6y | ||||||
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Title | Hypothetical protein YfdW from E. coli bound to Coenzyme A | ||||||
Components | Hypothetical protein yfdW | ||||||
Keywords | TRANSFERASE / intertwined dimer / structural genomics / Coenzyme A / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cellular response to acidic pH Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Gogos, A. / Gorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of Escherichia coli YfdW, a type III CoA transferase. Authors: Gogos, A. / Gorman, J. / Shapiro, L. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUES SER2 AND LEU3 ARISE FROM A CLONING ARTIFACT THAT RESULTS IN A 2 AMINO ACID ...SEQUENCE RESIDUES SER2 AND LEU3 ARISE FROM A CLONING ARTIFACT THAT RESULTS IN A 2 AMINO ACID INSERTION. RESIDUE NUMBERS AFTER THIS INSERTION ARE EQUAL TO 2 PLUS THE CORRECT RESIDUE NUMBER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q6y.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q6y.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q6y_validation.pdf.gz | 754.7 KB | Display | wwPDB validaton report |
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Full document | 1q6y_full_validation.pdf.gz | 761.1 KB | Display | |
Data in XML | 1q6y_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1q6y_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q6y ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q6y | HTTPS FTP |
-Related structure data
Related structure data | 1pqySC 1q7eC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 47236.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFDW / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / References: UniProt: P69902 | ||
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#2: Chemical | ChemComp-COA / | ||
#3: Chemical | ChemComp-MPD / ( #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 65% MPD, 0.1 M Bis-Tris pH 6.5, 1.5 mM CoA, 1.5 mM oxalate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→20 Å / Num. all: 27082 / Num. obs: 27082 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.066 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5 / Num. unique all: 2082 / Rsym value: 0.265 / % possible all: 72.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1pqy Resolution: 1.99→19.78 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.99→19.78 Å
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Refine LS restraints |
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