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Yorodumi- PDB-3ixm: Structure of the Gly74Cys mutant of arylmalonate decarboxylase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ixm | ||||||
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Title | Structure of the Gly74Cys mutant of arylmalonate decarboxylase in the sulfate ion associated form | ||||||
Components | Arylmalonate decarboxylase | ||||||
Keywords | LYASE / enantioselective racemase / Decarboxylase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bordetella bronchiseptica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nakasako, M. / Obata, R. | ||||||
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 | 3ixm.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ixm.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ixm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ixm_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 3ixm_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 3ixm_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3ixm_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ixm ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ixm | HTTPS FTP |
-Related structure data
Related structure data | 3dtvSC 3ixlC C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 24801.449 Da / Num. of mol.: 1 / Mutation: G74C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: KU1201 / Plasmid: pAMD101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.2M ammonium sulfate, 15%(w/v) glycerol, 0.1M HEPES, pH 6.2, 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: BL26B1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2008 / Details: mirror |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. obs: 16054 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.053 / Num. measured all: 174138 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.129 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DTV Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.484 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.165 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.296 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Total num. of bins used: 20
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