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- PDB-2vtz: Biosynthetic thiolase from Z. ramigera. Complex of the C89A mutan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vtz | ||||||
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Title | Biosynthetic thiolase from Z. ramigera. Complex of the C89A mutant with coenzyme A. | ||||||
![]() | ACETYL-COA ACETYLTRANSFERASE | ||||||
![]() | TRANSFERASE / ACYLTRANSFERASE / PHB BIOSYNTHESIS / THIOLASE FOLD | ||||||
Function / homology | ![]() poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid beta-oxidation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kursula, P. / Merilainen, G. / Wierenga, R.K. | ||||||
![]() | ![]() Title: The Sulfur Atoms of the Substrate Coa and the Catalytic Cysteine are Required for a Productive Mode of Substrate Binding in Bacterial Biosynthetic Thiolase, a Thioester-Dependent Enzyme. Authors: Merilainen, G. / Schmitz, W. / Wierenga, R.K. / Kursula, P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.6 KB | Display | ![]() |
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PDB format | ![]() | 246.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 64.4 KB | Display | |
Data in CIF | ![]() | 90.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vu0C ![]() 2vu1C ![]() 2vu2C ![]() 1m3zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 40509.145 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-392 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 89 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 89 TO ALA ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.2 % / Description: NONE |
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Crystal grow | pH: 5 / Details: pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 87692 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.8 / % possible all: 86.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M3Z Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.841 / SU B: 13.354 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.241 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.916 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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