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Yorodumi- PDB-4ktf: Crystal structure of Mycobacterium tuberculosis CYP121 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ktf | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4,4'-(3-amino-1H-pyrazole-4,5-diyl)diphenol | ||||||
Components | Cytochrome P450 121 | ||||||
Keywords | OXIDOREDUCTASE / P450 / cYY / C-C bond formation / Assumed cytosol | ||||||
Function / homology | Cytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / 4,4'-(3-amino-1H-pyrazole-4,5-diyl)diphenol / PROTOPORPHYRIN IX CONTAINING FE / : Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Hudson, S.A. | ||||||
Citation | Journal: Chemmedchem / Year: 2013 Title: Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121. Authors: Hudson, S.A. / Surade, S. / Coyne, A.G. / McLean, K.J. / Leys, D. / Munro, A.W. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ktf.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ktf.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ktf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4ktf ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4ktf | HTTPS FTP |
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-Related structure data
Related structure data | 4ktjC 4ktkC 4ktlC 1n40S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43174.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2276, RVBD_2276 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: I6YD01, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-1TM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2M Ammonium sulfate, 0.1M Sodium cacodylate-HCl, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91731 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91731 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→36.82 Å / Num. all: 96128 / Num. obs: 96128 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 14436 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1N40 Resolution: 1.35→35.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.796 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.052 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.715 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→35.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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