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Yorodumi- PDB-3fcd: Crystal Structure of a putative glyoxalase from an environmental ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fcd | ||||||
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Title | Crystal Structure of a putative glyoxalase from an environmental bacteria | ||||||
Components | Lyase | ||||||
Keywords | LYASE / lactoylglutathione lyase / YecM / 11004a / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / Orf125EGC139 Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Silberstein, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of a putative glyoxalase from an environmental bacteria Authors: Silberstein, M. / Eswaramoorthy, S. / 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 | 3fcd.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fcd.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/3fcd ftp://data.pdbj.org/pub/pdb/validation_reports/fc/3fcd | 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: 15442.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CODON+RIL / References: UniProt: Q93AH5 #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: 1.96 Å3/Da / Density % sol: 37.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350; 0.1M Bis-TRIS; sodium fluoride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 17538 / Num. obs: 17538 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.282 / Num. unique all: 1222 / % possible all: 66.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.92→35.64 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.92→35.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.038
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