+Open data
-Basic information
Entry | Database: PDB / ID: 1zpd | ||||||
---|---|---|---|---|---|---|---|
Title | PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS | ||||||
Components | PYRUVATE DECARBOXYLASE | ||||||
Keywords | ALCOHOL FERMENTATION / THIAMIN DIPHOSPHATE / DECARBOXYLASE | ||||||
Function / homology | Function and homology information pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Zymomonas mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Lu, G. / Dobritzsch, D. / Schneider, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases. Authors: Dobritzsch, D. / Konig, S. / Schneider, G. / Lu, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zpd.cif.gz | 483.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zpd.ent.gz | 390.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zpd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1zpd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1zpd_validation.xml.gz | 101.2 KB | Display | |
Data in CIF | 1zpd_validation.cif.gz | 154.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/1zpd ftp://data.pdbj.org/pub/pdb/validation_reports/zp/1zpd | HTTPS FTP |
-Related structure data
Related structure data | 1ypd S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 60957.281 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Culture collection (production host): ATCC 29191 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009/PREP4 / References: UniProt: P06672, pyruvate decarboxylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-DPX / #4: Chemical | ChemComp-CIT / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: pH 6.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→22.8 Å / Num. obs: 157263 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 1.91 % / Biso Wilson estimate: 10.41 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.86→1.91 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.6 / % possible all: 62.5 |
Reflection | *PLUS % possible obs: 88.2 % / Num. measured all: 306481 |
Reflection shell | *PLUS % possible obs: 51.7 % / Num. unique obs: 13826 / Num. measured obs: 25442 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YPD 1ypd Resolution: 1.86→15 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: NCS RESTRAINTS WERE APPLIED TO PROTEIN ATOMS AND MOST WATER MOLECULES WITH CHAIN ID W, U, V, AND X, WHICH SATISFY ALL THE NCS OPERATIONS. WATER MOLECULES WITH CHAIN ID Y SATISFY 3 OF 4 NCS ...Details: NCS RESTRAINTS WERE APPLIED TO PROTEIN ATOMS AND MOST WATER MOLECULES WITH CHAIN ID W, U, V, AND X, WHICH SATISFY ALL THE NCS OPERATIONS. WATER MOLECULES WITH CHAIN ID Y SATISFY 3 OF 4 NCS OPERATIONS WHILE WATERS WITH CHAIN ID Z SATISFY 2 OF 4 NCS'S. WATERS WITH CHAIN ID S DOES NOT FOLLOW ANY NCS OPERATIONS. ESD FROM SIGMAA (A) : 0.15
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 157061 / Rfactor obs: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|