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Yorodumi- PDB-2whf: Interaction of Mycobacterium tuberculosis CYP130 with heterocycli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2whf | ||||||
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Title | Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines | ||||||
Components | PUTATIVE CYTOCHROME P450 130 | ||||||
Keywords | OXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / HYPOTHETICAL PROTEIN | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cell wall / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / peptidoglycan-based cell wall / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Podust, L.M. / Ouellet, H. / von Kries, J.P. / Ortiz de Montellano, P.R. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2009 Title: Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines. Authors: Podust, L.M. / Ouellet, H. / von Kries, J.P. / de Montellano, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2whf.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2whf.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 2whf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2whf_validation.pdf.gz | 819 KB | Display | wwPDB validaton report |
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Full document | 2whf_full_validation.pdf.gz | 828 KB | Display | |
Data in XML | 2whf_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2whf_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2whf ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2whf | HTTPS FTP |
-Related structure data
Related structure data | 2wgyC 2wh8C 2uuqS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 45705.566 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): HMS174 References: UniProt: Q11062, UniProt: P9WPN5*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | 6 HIS-TAG RESIDUES ARE ADDED AT THE N-TERMINUS. A 406 SER AND A 407 ARG ARE INTRODUCED AT THE C- ...6 HIS-TAG RESIDUES ARE ADDED AT THE N-TERMINUS. A 406 SER AND A 407 ARG ARE INTRODUCED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.3 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 20% PEG 4000, 0.1M NA ACETATE, PH 5.5; 3% ISOPROPYL ALCOHOL |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 14, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 51244 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UUQ Resolution: 1.58→79.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.117 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
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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: 25.131 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→79.81 Å
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Refine LS restraints |
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