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Yorodumi- PDB-1ted: Crystal structure of a type III polyketide synthase PKS18 from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ted | ||||||
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Title | Crystal structure of a type III polyketide synthase PKS18 from Mycobacterium tuberculosis | ||||||
Components | pks18 | ||||||
Keywords | TRANSFERASE / thiolase fold / substrate binding tunnel | ||||||
Function / homology | Function and homology information chalcone biosynthetic process / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Sankaranarayanan, R. / Shanmugam, V.M. / Rukmini, R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: A novel tunnel in mycobacterial type III polyketide synthase reveals the structural basis for generating diverse metabolites Authors: Sankaranarayanan, R. / Saxena, P. / Marathe, U.B. / Gokhale, R.S. / Shanmugam, V.M. / Rukmini, R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray crystallographic investigations of an unusual type III polyketide synthase PKS18 from Mycobacterium tuberculosis Authors: Rukmini, R. / Shanmugam, V.M. / Saxena, P. / Gokhale, R.S. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ted.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ted.ent.gz | 242.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ted.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ted_validation.pdf.gz | 475.4 KB | Display | wwPDB validaton report |
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Full document | 1ted_full_validation.pdf.gz | 536.1 KB | Display | |
Data in XML | 1ted_validation.xml.gz | 71.9 KB | Display | |
Data in CIF | 1ted_validation.cif.gz | 101.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/1ted ftp://data.pdbj.org/pub/pdb/validation_reports/te/1ted | HTTPS FTP |
-Related structure data
Related structure data | 1teeC 1cgzS 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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Details | The biological assembly is a homodimer. The file contains two of them, AB and CD. |
-Components
#1: Protein | Mass: 42073.316 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pks18 / Plasmid: pET21C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q7D8I1, UniProt: P9WPF1*PLUS, chalcone synthase #2: Chemical | ChemComp-MYR / #3: 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: 2.5 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: PEG 8000, HEPES, ethylene glycol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25 Å / Num. all: 80874 / Num. obs: 76912 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.74 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.25→2.36 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2 / Num. unique all: 7360 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CGZ Resolution: 2.25→24.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1677848.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9511 Å2 / ksol: 0.328374 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→24.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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