+Open data
-Basic information
Entry | Database: PDB / ID: 2gdr | ||||||
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Title | Crystal structure of a bacterial glutathione transferase | ||||||
Components | glutathione S-transferase | ||||||
Keywords | TRANSFERASE / protein homodimer / each monomer contains two domains / N-term domain is mixed beta sheets and alpha helices / C-term domain is alpha helical | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tocheva, E.I. / Fortin, P.D. / Eltis, L.D. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structures of Ternary Complexes of BphK, a Bacterial Glutathione S-Transferase That Reductively Dechlorinates Polychlorinated Biphenyl Metabolites. Authors: Tocheva, E.I. / Fortin, P.D. / Eltis, L.D. / Murphy, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gdr.cif.gz | 243.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gdr.ent.gz | 199.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/2gdr ftp://data.pdbj.org/pub/pdb/validation_reports/gd/2gdr | HTTPS FTP |
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-Related structure data
Related structure data | 2dsaC 2gdh S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22268.111 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: bphK / Production host: Escherichia coli (E. coli) References: GenBank: 27528348, UniProt: Q59721*PLUS, glutathione transferase #2: Chemical | ChemComp-GSH / #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: 3.03 Å3/Da / Density % sol: 59.41 % |
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Crystal grow | Temperature: 323 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1M K/Na tartrate, 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 323K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97974 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97974 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 92159 / Num. obs: 92159 / % possible obs: 97 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.384 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GDH 2gdh Resolution: 2.1→50 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber Details: The twinning operator is h,-h-k,-l. The twinning fraction is 0.45.
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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LS refinement shell | Resolution: 2.1→2.18 Å / Num. reflection Rfree: 334 |