+Open data
-Basic information
Entry | Database: PDB / ID: 2vlb | ||||||
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Title | Structure of unliganded arylmalonate decarboxylase | ||||||
Components | ARYLMALONATE DECARBOXYLASE | ||||||
Keywords | LYASE / PROTEIN DYNAMICS / AMDASE / DECARBOXYLASE / DECARBOXYLATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BORDETELLA BRONCHISEPTICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.92 Å | ||||||
Authors | Kuettner, E.B. / Keim, A. / Kircher, M. / Rosmus, S. / Strater, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Active Site Mobility Revealed by the Crystal Structure of Arylmalonate Decarboxylase from Bordetella Bronchiseptica Authors: Kuettner, E.B. / Keim, A. / Kircher, M. / Rosmus, S. / Strater, N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vlb.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vlb.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vlb ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vlb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25970.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: IN ALL PROTEIN CHAINS, C148 AND C188 ARE LINKED TO BETA-MERCAPTO ETHANOL Source: (gene. exp.) BORDETELLA BRONCHISEPTICA (bacteria) / Description: ALCALIGENES BRONCHISEPTICUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 (DH10B) (INVITROGEN) / References: UniProt: Q05115, arylmalonate decarboxylase #2: Chemical | ChemComp-BME / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Nonpolymer details | 1,2-ETHANEDIOL (EDO): ORIGINATES FROM CRYSTAL CRYO PROTECTION SOLUTION. BETA-MERCAPTOETHANOL (BME): ...1,2-ETHANEDIOL | |
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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: HANGING-DROP VAPOUR-DIFFUSION SETUP WITH 0.5 ML RESERVOIR SOLUTION AT 292 K. DROPS COMPOSED OF 1 MICROLITER OF PROTEIN AND RESERVOIR SOLUTIONS EACH. PROTEIN SOLUTION CONTAINS 7-8 MG/ML ...Details: HANGING-DROP VAPOUR-DIFFUSION SETUP WITH 0.5 ML RESERVOIR SOLUTION AT 292 K. DROPS COMPOSED OF 1 MICROLITER OF PROTEIN AND RESERVOIR SOLUTIONS EACH. PROTEIN SOLUTION CONTAINS 7-8 MG/ML AMDASE, 20 MM TRIS-HCL PH 8 AND 0.5 MM BETA-MERCAPTO ETHANOL. RESERVOIR SOLUTION CONTAINS 1.4-1.8 M NA/K PHOSPHATE PH 5.8-6.4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2006 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→30 Å / Num. obs: 89247 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.92→2.02 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.2 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.92→29.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.529 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / 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: 44.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→29.64 Å
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Refine LS restraints |
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