+Open data
-Basic information
Entry | Database: PDB / ID: 2iwy | ||||||
---|---|---|---|---|---|---|---|
Title | Human mitochondrial beta-ketoacyl ACP synthase | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE | ||||||
Keywords | TRANSFERASE / MITOCHONDRIA / MITOCHONDRION / LIPID SYNTHESIS / FATTY ACID SYNTHESIS / FATTY ACID BIOSYNTHESIS / BETA-KETOACYL ACP SYNTHASE / TRANSIT PEPTIDE / ACYLTRANSFERASE / CLAISEN CONDENSATION / KAS / CERULENIN / HOMO SAPIENS | ||||||
Function / homology | Function and homology information short-chain fatty acid biosynthetic process / medium-chain fatty acid biosynthetic process / acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Mitochondrial protein degradation / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Christensen, C.E. / Kragelund, B.B. / von Wettstein-Knowles, P. / Henriksen, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structure of the Human Beta-Ketoacyl [Acp] Synthase from the Mitochondrial Type II Fatty Acid Synthase. Authors: Christensen, C.E. / Kragelund, B.B. / von Wettstein-Knowles, P. / Henriksen, A. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Cloning, Expression, and Characterization of the Human Mitochondrial Beta-Ketoacyl Synthase Authors: Zhang, L. / Joshi, A.K. / Hofmann, J. / Schweizer, E. / Smith, S. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2iwy.cif.gz | 175.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2iwy.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 2iwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iwy_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2iwy_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 2iwy_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2iwy_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/2iwy ftp://data.pdbj.org/pub/pdb/validation_reports/iw/2iwy | HTTPS FTP |
-Related structure data
Related structure data | 2iwzC 2ix4C 1w0iS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46439.566 Da / Num. of mol.: 2 / Fragment: RESIDUES 38-459 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: SUMIO SUGANO, UNIVERSITY OF TOKYO / Plasmid: PQE30 / Production host: Escherichia coli M15 (bacteria) / Variant (production host): PREP4 References: UniProt: Q9NWU1, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | GENETICALL | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % |
---|---|
Crystal grow | pH: 7.8 / Details: 24% PEG-3350, 0.2 M NH4CL, pH 7.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.063 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.063 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.9 Å / Num. obs: 51373 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / % possible all: 96.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W0I Resolution: 2.06→36.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.59 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: DISORDERED SIDE CHAINS ARE NOT INCLUDE IN THE THE MODEL.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→36.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|