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Yorodumi- PDB-2bui: E. COLI BETA-KETOACYL (ACYL CARRIER PROTEIN) SYNTHASE I IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bui | |||||||||
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Title | E. COLI BETA-KETOACYL (ACYL CARRIER PROTEIN) SYNTHASE I IN COMPLEX WITH OCTANOIC ACID, 120K | |||||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I | |||||||||
Keywords | SYNTHASE / FATTY ACID SYNTHASE / THIOLASE FOLD / CLAISEN CONDENSATION / TRANSFERASE | |||||||||
Function / homology | Function and homology information monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Olsen, J.G. / Von Wettstein-Knowles, P. / Henriksen, A. | |||||||||
Citation | Journal: FEBS J. / Year: 2006 Title: Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases. Authors: von Wettstein-Knowles, P. / Olsen, J.G. / McGuire, K.A. / Henriksen, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bui.cif.gz | 314.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bui.ent.gz | 256.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/2bui ftp://data.pdbj.org/pub/pdb/validation_reports/bu/2bui | HTTPS FTP |
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-Related structure data
Related structure data | 1h4fC 2buhC 2bywC 2byxC 2byyC 2byzC 2bz3C 2bz4C 1ek8S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42656.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THIOESTER LINK BETWEEN CYS 163 AND C1 IN OCTANOIC ACID Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP) References: UniProt: P14926, UniProt: P0A953*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-NH4 / #3: Chemical | ChemComp-OCA / #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: ACYL-[ACYL-CARRIER PROTEIN] + MALONYL-[ACYL- CARRIER PROTEIN] = 3-OXOACYL-[ACYL- ...CATALYTIC ACTIVITY: ACYL-[ACYL-CARRIER PROTEIN] + MALONYL-[ACYL- CARRIER PROTEIN] = 3-OXOACYL-[ACYL-CARRIER PROTEIN] + CO(2) + [ACYL-CARRIER PROTEIN]. | |
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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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 7.4 Details: 2% PEG 400, 1.9 M AMMONIUM SULPHATE,0.1 M BIS-TRIS PROPANE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 4, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→14.98 Å / Num. obs: 67445 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.4→2.57 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EK8 Resolution: 2.4→14.98 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.3354 Å2 / ksol: 0.410858 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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