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Yorodumi- PDB-4di8: CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4di8 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5 | |||||||||
Components | 2-pyrone-4,6-dicarbaxylate hydrolase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information 2-pyrone-4,6-dicarboxylate lactonase / 2-pyrone-4,6-dicarboxylate lactonase activity / 3,4-dihydroxybenzoate catabolic process / lignin catabolic process Similarity search - Function | |||||||||
Biological species | Sphingomonas paucimobilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å | |||||||||
Authors | Malashkevich, V.N. / Toro, R. / Hobbs, M.E. / Raushel, F.M. / Almo, S.C. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structure and Catalytic Mechanism of LigI: Insight into the Amidohydrolase Enzymes of cog3618 and Lignin Degradation. Authors: Hobbs, M.E. / Malashkevich, V. / Williams, H.J. / Xu, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4di8.cif.gz | 252.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4di8.ent.gz | 203.1 KB | Display | PDB format |
PDBx/mmJSON format | 4di8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/4di8 ftp://data.pdbj.org/pub/pdb/validation_reports/di/4di8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | monomer |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33986.762 Da / Num. of mol.: 2 / Mutation: D246A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: SYK-6 / Gene: ligI / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: O87170 |
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-Non-polymers , 5 types, 683 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.17 Å3/Da / Density % sol: 43.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% peg 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Na-acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.81→50 Å / Num. obs: 53516 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Χ2: 1.509 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 45.19 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→19.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1756 / WRfactor Rwork: 0.1489 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 5.003 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1242 / SU Rfree: 0.1123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES: WITH TLS ADDED. 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 max: 57.5 Å2 / Biso mean: 17.2451 Å2 / Biso min: 6.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
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Refinement TLS params. | T12: 0.0012 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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