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Yorodumi- PDB-1hzp: Crystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hzp | ||||||
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Title | Crystal Structure of the Myobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Synthase III | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III | ||||||
Keywords | TRANSFERASE / fatty acid biosynthesis / myobacterium tuberculosis / structural basis for substrate specificity / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information mycobacterial beta-ketoacyl-[acyl carrier protein] synthase III / beta-ketodecanoyl-[acyl-carrier-protein] synthase activity / long-chain fatty-acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / fatty-acyl-CoA binding / fatty acid elongation / lipid biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Scarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III Authors: Scarsdale, J.N. / Kazanina, G. / He, X. / Reynolds, K.A. / Wright, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hzp.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hzp.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 1hzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/1hzp ftp://data.pdbj.org/pub/pdb/validation_reports/hz/1hzp | HTTPS FTP |
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-Related structure data
Related structure data | 1eblS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34903.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS References: UniProt: P0A574, UniProt: P9WNG3*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-DAO / | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 43.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: PEG4000, Tris/HCl. 300mM NaCl, glycerol, 10mM CaCl2, pH 8.0, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: Osmic Confocal optics |
Radiation | Monochromator: Osmic Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99 Å / Num. all: 37716 / Num. obs: 37503 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1860 / % possible all: 99 |
Reflection shell | *PLUS % possible obs: 82 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: poly alanine chain based on residues 1-317 from E Coli FabH (RCSB entry 1EBL) Resolution: 2.1→30.38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 797513.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.46 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.319 / % reflection Rfree: 10 % / Rfactor Rwork: 0.281 / Rfactor obs: 0.281 |