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Yorodumi- PDB-3st6: Structure of a M. tuberculosis Synthase, MbtI, in Complex with an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3st6 | ||||||
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Title | Structure of a M. tuberculosis Synthase, MbtI, in Complex with an Isochorismate Analogue Inhibitor | ||||||
Components | Isochorismate synthase/isochorismate-pyruvate lyase mbtI | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / Structural Genomics / TB Structural Genomics Consortium / TBSGC / mixed alpha/beta fold / salicylate synthase / chorismate binding / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity ...isochorismate lyase / isochorismate pyruvate lyase activity / catechol-containing siderophore biosynthetic process / isochorismate synthase / isochorismate synthase activity / oxo-acid-lyase activity / salicylic acid biosynthetic process / cellular response to iron ion starvation / chorismate mutase / chorismate mutase activity / response to host immune response / tryptophan biosynthetic process / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Chi, G. / Bulloch, E.M.M. / Manos-Turvey, A. / Payne, R.J. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis Authors: Chi, G. / Manos-Turvey, A. / O'Connor, P.D. / Johnston, J.M. / Evans, G.L. / Baker, E.N. / Payne, R.J. / Lott, J.S. / Bulloch, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3st6.cif.gz | 351.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3st6.ent.gz | 280.8 KB | Display | PDB format |
PDBx/mmJSON format | 3st6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3st6_validation.pdf.gz | 476.7 KB | Display | wwPDB validaton report |
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Full document | 3st6_full_validation.pdf.gz | 502.2 KB | Display | |
Data in XML | 3st6_validation.xml.gz | 69.6 KB | Display | |
Data in CIF | 3st6_validation.cif.gz | 100.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/3st6 ftp://data.pdbj.org/pub/pdb/validation_reports/st/3st6 | HTTPS FTP |
-Related structure data
Related structure data | 3rv6C 3rv7C 3rv8C 3rv9C 3vehC 2g5fS 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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Unit cell |
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-Components
#1: Protein | Mass: 48811.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2386c / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21:DE3 References: UniProt: Q7D785, UniProt: P9WFX1*PLUS, Lyases; Carbon-carbon lyases; Oxo-acid-lyases, isochorismate synthase #2: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 17% PEG 6000, malic acid/KOH, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.542 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2011 |
Radiation | Monochromator: Two Si111 Crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.36 Å / Num. obs: 243093 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 26.04 Å2 |
Reflection shell | Resolution: 1.6→1.69 Å / Mean I/σ(I) obs: 1 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G5F Resolution: 1.75→29.36 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9212 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 121.82 Å2 / Biso mean: 32.81 Å2 / Biso min: 8.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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