+Open data
-Basic information
Entry | Database: PDB / ID: 3log | ||||||
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Title | Crystal structure of MbtI from Mycobacterium tuberculosis | ||||||
Components | Isochorismate synthase/isochorismate-pyruvate lyase mbtI | ||||||
Keywords | ISOMERASE / chorismate / salicylate / anthranilate / isochorismate / isochorismate synthase / isochorismate lyase / Ion transport / Lyase / Metal-binding / Multifunctional enzyme / Transport | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Bulloch, E.M.M. / Lott, J.S. / Baker, E.N. / Johnston, J.M. | ||||||
Citation | Journal: Chemmedchem / Year: 2010 Title: Inhibition studies of Mycobacterium tuberculosis salicylate synthase (MbtI). Authors: Manos-Turvey, A. / Bulloch, E.M. / Rutledge, P.J. / Baker, E.N. / Lott, J.S. / Payne, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3log.cif.gz | 383.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3log.ent.gz | 307.2 KB | Display | PDB format |
PDBx/mmJSON format | 3log.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/3log ftp://data.pdbj.org/pub/pdb/validation_reports/lo/3log | HTTPS FTP |
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-Related structure data
Related structure data | 2g5fS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48827.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mbtI, MT2454, Rv2386c / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21:DE3 p540/542 References: UniProt: Q7D785, UniProt: P9WFX1*PLUS, isochorismate synthase, Lyases; Carbon-carbon lyases; Oxo-acid-lyases |
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-Non-polymers , 5 types, 1636 molecules
#2: Chemical | ChemComp-SIN / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-CO3 / | #6: 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: 2.44 Å3/Da / Density % sol: 49.65 % / Mosaicity: 0.657 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 14% MPEG 5000, 0.2M succinic acid, KOH pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→93.66 Å / Num. all: 189008 / Num. obs: 189003 / % possible obs: 97 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.061 / Χ2: 1.312 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.24 / Num. unique all: 16853 / Χ2: 0.929 / % possible all: 86.8 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G5F Resolution: 1.73→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.853 / SU R Cruickshank DPI: 0.116 / SU Rfree: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.02 Å2 / Biso mean: 36.059 Å2 / Biso min: 18.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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