+Open data
-Basic information
Entry | Database: PDB / ID: 3dtv | ||||||
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Title | Crystal structure of arylmalonate decarboxylase | ||||||
Components | (Arylmalonate ...) x 3 | ||||||
Keywords | LYASE / ENANTIOSELECTIVE DECARBOXYLATION / Decarboxylase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å | ||||||
Authors | Nakasako, M. / Obata, R. / Miyamaoto, K. / Ohta, H. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural Basis for Inverting the Enantioselectivity of Arylmalonate Decarboxylase Revealed by the Structural Analysis of the Gly74Cys/Cys188Ser Mutant in the Liganded Form Authors: Obata, R. / Nakasako, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus Authors: Nakasako, M. / Obata, R. / Okubo, R. / Nakayama, S. / Miyamoto, K. / Ohta, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dtv.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dtv.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/3dtv ftp://data.pdbj.org/pub/pdb/validation_reports/dt/3dtv | 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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3 |
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4 |
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5 |
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Unit cell |
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Details | THOUGH FOUR MOLECULES OCCUPIED THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, SMALL-ANGLE X=RAY SCATTERING MEASUREMENT OF THE ENZYME SOLUTION REVEALED THAT THE FUNCTIONAL UNIT OF THE ENZYME IN SOLUTION WAS MONOMER. THIS POINT IS REPORTED IN REFERENCE 1 OF REMARK 1 |
-Components
-Arylmalonate ... , 3 types, 4 molecules ABCD
#1: Protein | Mass: 24755.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: KU1201 / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase | ||
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#2: Protein | Mass: 24831.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase #3: Protein | | Mass: 24831.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase |
-Non-polymers , 4 types, 378 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-BME / | #7: 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: 2.9 Å3/Da / Density % sol: 57.58 % Description: DATA WERE COLLECTED USING THE OSCIALLTION METHOD |
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Crystal grow | Temperature: 293 K / pH: 8 Details: 1.5M ammonium sulfate, 12%(W/V) glycerol, 0.1M Tris-HCl pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2007 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 68279 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.949 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.64 / ESU R Free: 0.171
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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