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Yorodumi- PDB-2v6k: Structure of Maleyl Pyruvate Isomerase, a bacterial glutathione-s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v6k | ||||||
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Title | Structure of Maleyl Pyruvate Isomerase, a bacterial glutathione-s- transferase in Zeta class, in complex with substrate analogue dicarboxyethyl glutathione | ||||||
Components | MALEYLPYRUVATE ISOMERASE | ||||||
Keywords | ISOMERASE / GLUTATHIONE-S-TRANSFERASE / GST / PLASMID / PYRUVATE / BACTERIAL / BIODEGRADATION / MALEYL PYRUVATE / FUMARYL PYRUVATE | ||||||
Function / homology | Function and homology information maleylpyruvate isomerase / maleylpyruvate isomerase activity / naphthalene catabolic process / maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase activity / glutathione metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | RALSTONIA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Shoemark, D.K. / Zhou, N.-Y. / Williams, P.A. / Hadfield, A.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of Bacterial Glutathione-S-Transferase Maleyl Pyruvate Isomerase and Implications for Mechanism of Isomerisation. Authors: Marsh, M. / Shoemark, D.K. / Jacob, A. / Robinson, C. / Cahill, B. / Zhou, N.-Y. / Williams, P.A. / Hadfield, A.T. #1: Journal: J.Bacteriol. / Year: 1998 Title: A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas Sp. Strain U2 Authors: Fuenmayor, S.L. / Wild, M. / Williams, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v6k.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v6k.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v6k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2v6k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2v6k_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 2v6k_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/2v6k ftp://data.pdbj.org/pub/pdb/validation_reports/v6/2v6k | HTTPS FTP |
-Related structure data
Related structure data | 2jl4C 2c1r 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9939, -0.000248, -0.1099), Vector: |
-Components
#1: Protein | Mass: 23732.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RALSTONIA SP. (bacteria) / Strain: U2 / Plasmid: PET 28 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: O86043, maleylacetoacetate isomerase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL LYSINE VISIBLE WHICH COMES FROM HIS-TAG | |
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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: 2.72 Å3/Da / Density % sol: 55 % Description: DATA WERE 99 PERCENT COMPLETE TO 1.5 A. THE MODEL WAS REFINED AGAINST DATA TO 1.3 A RESOLUTION, 44 PERCENT COMPLETE IN THE OUTER SHELL. |
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Crystal grow | pH: 7.5 Details: MOTHER LIQOUR: RESERVOIR SOLUTION: DROP: 1 UL MOTHERLIQUOR, I UL RESERVOIR, 1 UL BENZAMIDINE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→27.6 Å / Num. obs: 394142 / % possible obs: 74.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.2→1.27 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 11.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C1R 2c1r Resolution: 1.3→43.11 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.035 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→43.11 Å
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Refine LS restraints |
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