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Yorodumi- PDB-2wgg: Crystal Structure of Mycobacterium tuberculosis C171Q KasA varian... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wgg | ||||||
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Title | Crystal Structure of Mycobacterium tuberculosis C171Q KasA variant with bound TLM | ||||||
Components | 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 | ||||||
Keywords | TRANSFERASE / BETA KETOACYL SYNTHASE I / CYTOPLASM / ACYLTRANSFERASE / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I / fatty acid elongation, saturated fatty acid / fatty acid elongation / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Luckner, S.R. / Kisker, C. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Crystal Structures of Mycobacterium Tuberculosis Kasa Show Mode of Action within Cell Wall Biosynthesis and its Inhibition by Thiolactomycin Authors: Luckner, S.R. / Machutta, C.A. / Tonge, P.J. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wgg.cif.gz | 621.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wgg.ent.gz | 516.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wgg_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2wgg_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2wgg_validation.xml.gz | 123.9 KB | Display | |
Data in CIF | 2wgg_validation.cif.gz | 169.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/2wgg ftp://data.pdbj.org/pub/pdb/validation_reports/wg/2wgg | HTTPS FTP |
-Related structure data
Related structure data | 2wgdSC 2wgeC 2wgfC 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 43384.969 Da / Num. of mol.: 8 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155 References: UniProt: P63454, UniProt: P9WQD9*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I |
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-Non-polymers , 5 types, 961 molecules
#2: Chemical | ChemComp-TLM / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-2PE / #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 171 TO GLN ENGINEERED RESIDUE IN CHAIN B, CYS 171 TO GLN ...ENGINEERED |
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Sequence details | CYS 171 IS MUTATED TO GLN 171 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.74 % / Description: NONE |
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Crystal grow | Details: PEG3350, POTASSIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.287 |
Reflection | Resolution: 2→46.18 Å / Num. obs: 996668 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.89 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.35 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WGD Resolution: 2→46.16 Å / σ(F): 1.08 / Phase error: 26.89 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.68 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.16 Å
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Refine LS restraints |
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LS refinement shell |
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