2VBI
Holostructure of pyruvate decarboxylase from Acetobacter pasteurianus
- PDB DOI: https://doi.org/10.2210/pdb2VBI/pdb
- Classification: LYASE
- Organism(s): Acetobacter pasteurianus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2007-09-14 Released: 2008-04-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.243 
- R-Value Work: 0.224 
- R-Value Observed: 0.225 
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
This is version 1.3 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PYRUVATE DECARBOXYLASE | 566 | Acetobacter pasteurianus | Mutation(s): 0  EC: 4.1.1.1 | ||
UniProt | |||||
Find proteins for Q8L388 (Acetobacter pasteurianus) Explore Q8L388  Go to UniProtKB:  Q8L388 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8L388 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
TPP Query on TPP | J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] | THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O | |||
MG Query on MG | I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.243 
- R-Value Work: 0.224 
- R-Value Observed: 0.225 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 179.619 | α = 90 |
b = 162.434 | β = 102.71 |
c = 169.331 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2008-04-08  Deposition Author(s): Gocke, D., Berthold, C.L., Schneider, G., Pohl, M.
Revision History (Full details and data files)
- Version 1.0: 2008-04-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2018-01-17
Changes: Data collection - Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description