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Yorodumi- PDB-2vbf: The holostructure of the branched-chain keto acid decarboxylase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vbf | ||||||
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Title | The holostructure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis | ||||||
Components | BRANCHED-CHAIN ALPHA-KETOACID DECARBOXYLASE | ||||||
Keywords | LYASE / KDCA / FLAVOPROTEIN / THDP-DEPENDENT ENZYMES / THIAMINE PYROPHOSPHATE | ||||||
Function / homology | Function and homology information branched-chain-2-oxoacid decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / branched-chain amino acid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | LACTOCOCCUS LACTIS (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Berthold, C.L. / Gocke, D. / Wood, M.D. / Leeper, F. / Pohl, M. / Schneider, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) from Lactococcus Lactis Provides Insights Into the Structural Basis for the Chemo- and Enantioselective Carboligation Reaction Authors: Berthold, C.L. / Gocke, D. / Wood, M.D. / Leeper, F. / Pohl, M. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vbf.cif.gz | 252.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vbf.ent.gz | 200 KB | Display | PDB format |
PDBx/mmJSON format | 2vbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vbf_validation.pdf.gz | 968.7 KB | Display | wwPDB validaton report |
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Full document | 2vbf_full_validation.pdf.gz | 978.4 KB | Display | |
Data in XML | 2vbf_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 2vbf_validation.cif.gz | 76.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/2vbf ftp://data.pdbj.org/pub/pdb/validation_reports/vb/2vbf | HTTPS FTP |
-Related structure data
Related structure data | 2vbgC 1ovmS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 63406.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CHAIN A AND B CONTAIN THE COMPLETE ENZYME SEQUENCE AND SHORT N-TERMINAL TAGS WITH LINKERS, WHICH ARE BOUND IN ADJACENT DIMERS IN THE CRYSTAL. Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria) Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6QBS4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE PROTEIN CONTAINS A 23 AMINO ACID N-TERMINAL EXTENSION, MGSSHHHHHH | |
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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: 1.9 Å3/Da / Density % sol: 34.71 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2007 |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→56.17 Å / Num. obs: 127559 / % possible obs: 92.4 % / Observed criterion σ(I): 6 / Redundancy: 3.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 63.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OVM Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.674 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUES 182-187 HAVE NOT BEEN MODELED DUE TO LACK OF ELECTRON DENSITY THE FLEXIBLE REGION B 538-547 WAS MODELED AT OCCUPANCY 0.5
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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