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Yorodumi- PDB-2wkv: BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE N316D MUTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wkv | ||||||
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Title | BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE N316D MUTANT WITH COENZYME A. | ||||||
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: 2.5 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 | 2wkv.cif.gz | 572.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wkv.ent.gz | 471.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/2wkv ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wkv | HTTPS FTP |
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-Related structure data
Related structure data | 2wktC 2wkuC 2wl4C 2wl5C 2wl6C 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: 40542.191 Da / Num. of mol.: 4 / Fragment: 2-11,12-292 / 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)PLYSS / References: UniProt: P07097, acetyl-CoA C-acetyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-COA / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 316 TO ASP ENGINEERED RESIDUE IN CHAIN B, ASN 316 TO ASP ...ENGINEERED | Sequence details | A11 INSERTION AND A129R MUTATIONS WERE FOUND TO EXIST IN THE WILD TYPE CLONE USED AND ARE ALREADY ...A11 INSERTION AND A129R MUTATIONS WERE FOUND TO EXIST IN THE WILD TYPE CLONE USED AND ARE ALREADY DESCRIBED IN THE FIRST PUBLISHED STRUCTURE OF THIS ENZYME, (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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 5.7 Details: 1.9 M (NH4)2SO4, 0.1 M MES (PH 5.7), 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: Jun 26, 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: 2.5→20 Å / Num. obs: 69019 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DLU Resolution: 2.5→19.69 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 21.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.86 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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