+Open data
-Basic information
Entry | Database: PDB / ID: 3g7k | ||||||
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Title | Crystal Structure of Methylitaconate-delta-isomerase | ||||||
Components | 3-methylitaconate isomerase | ||||||
Keywords | ISOMERASE / DapF family fold / closed conformation / open conformation | ||||||
Function / homology | Function and homology information methylitaconate Delta-isomerase / methylitaconate delta-isomerase activity / nicotinate catabolic process Similarity search - Function | ||||||
Biological species | Eubacterium barkeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Messerschmidt, A. / Macieira, S. / Velarde, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri Authors: Velarde, M. / Macieira, S. / Hilberg, M. / Broker, G. / Tu, S.-M. / Golding, B.T. / Pierik, A.J. / Buckel, W. / Messerschmidt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g7k.cif.gz | 268.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g7k.ent.gz | 216 KB | Display | PDB format |
PDBx/mmJSON format | 3g7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g7k ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g7k | HTTPS FTP |
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-Related structure data
Related structure data | 2pw0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 41572.223 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium barkeri (bacteria) / Gene: Mii / Plasmid: pALD(EL)2-Kann(blue), pASG3_mii / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q0QLE6, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds #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: 2.59 Å3/Da / Density % sol: 52.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein solution: 150mM Tris/HCl, 150mM NaCl; Reservoir solution: 23% PEG 1500, 18% glycerol anhydrous. 0.001ml protein plus 0.001ml reservoir, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0707 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2008 Details: LN2 cooled fixed-exit, Si(111) monochromator; Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0707 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 47521 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.434 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PW0 Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.989 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 1.101 / ESU R Free: 0.343 / 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: 46.36 Å2
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Refine analyze | Luzzati coordinate error free: 0.298 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.703→2.773 Å / Total num. of bins used: 20
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