+Open data
-Basic information
Entry | Database: PDB / ID: 2wl6 | ||||||
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Title | BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. THE N316H-H348N MUTANT. | ||||||
Components | ACETYL-COA ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ACYLTRANSFERASE / PHB BIOSYNTHESIS / CYTOPLASM / THIOLASE FOLD | ||||||
Function / homology | Function and homology information poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ZOOGLOEA RAMIGERA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Merilainen, G. / Poikela, V. / Kursula, P. / Wierenga, R.K. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: The Thiolase Reaction Mechanism: The Importance of Asn316 and His348 for Stabilizing the Enolate Intermediate of the Claisen Condensation. Authors: Merilainen, G. / Poikela, V. / Kursula, P. / Wierenga, R.K. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wl6.cif.gz | 277.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wl6.ent.gz | 226.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/2wl6 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wl6 | HTTPS FTP |
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-Related structure data
Related structure data | 2wktC 2wkuC 2wkvC 2wl4C 2wl5C 1dluS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 40541.207 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-11,12-392 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZOOGLOEA RAMIGERA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P07097, acetyl-CoA C-acetyltransferase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 316 TO HIS ENGINEERED RESIDUE IN CHAIN A, HIS 348 TO ASN ...ENGINEERED | Sequence details | A11 INSERTION AND A129R MUTATION WERE FOUND TO EXIST IN THE WILD TYPE CLONE USED AND IS ALREADY ...A11 INSERTION AND A129R MUTATION WERE FOUND TO EXIST IN THE WILD TYPE CLONE USED AND IS ALREADY DESCRIBED IN THE FIRST STRUCTURE PUBLISHED FROM THIS ENZYME, IN THE ARTICLE (STRUCTURE 1999, 7:1279-1290) | |
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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.167 M SODIUM CITRATE (PH 6.5), 1.58 M (NH4)2SO4, 1 MM EDTA, 1 MM NAN3 AND 1 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→43.9 Å / Num. obs: 39685 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.98→3.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DLU Resolution: 2.98→37.42 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.755 / SU B: 22.712 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.98→37.42 Å
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Refine LS restraints |
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