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Yorodumi- PDB-7nqn: Mycobacterium tuberculosis Cytochrome P450 CYP121 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nqn | |||||||||
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Title | Mycobacterium tuberculosis Cytochrome P450 CYP121 in complex with lead compound 14 | |||||||||
Components | Mycocyclosin synthase | |||||||||
Keywords | METAL BINDING PROTEIN / Mycobacterium tuberculosis / Heme-binding / inhibitor / complex | |||||||||
Function / homology | Function and homology information mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Selvam, I.R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: A new strategy for hit generation: Novel in cellulo active inhibitors of CYP121A1 from Mycobacterium tuberculosis via a combined X-ray crystallographic and phenotypic screening approach (XP screen). Authors: Frederickson, M. / Selvam, I.R. / Evangelopoulos, D. / McLean, K.J. / Katariya, M.M. / Tunnicliffe, R.B. / Campbell, B. / Kavanagh, M.E. / Charoensutthivarakul, S. / Blankley, R.T. / Levy, C. ...Authors: Frederickson, M. / Selvam, I.R. / Evangelopoulos, D. / McLean, K.J. / Katariya, M.M. / Tunnicliffe, R.B. / Campbell, B. / Kavanagh, M.E. / Charoensutthivarakul, S. / Blankley, R.T. / Levy, C.W. / de Carvalho, L.P.S. / Leys, D. / Munro, A.W. / Coyne, A.G. / Abell, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nqn.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nqn.ent.gz | 148.6 KB | Display | PDB format |
PDBx/mmJSON format | 7nqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nqn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7nqn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7nqn_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 7nqn_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/7nqn ftp://data.pdbj.org/pub/pdb/validation_reports/nq/7nqn | HTTPS FTP |
-Related structure data
Related structure data | 7nqmC 7nqoC 1n40S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43305.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: cyp121, Rv2276, MTCY339.34c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP7, mycocyclosin synthase |
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-Non-polymers , 6 types, 654 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | ChemComp-UMT / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 3.5 M Ammonium sulphate, 1 M MES / PH range: 5 - 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2018 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.59903→67.6013 Å / Num. obs: 63141 / % possible obs: 98.8 % / Redundancy: 18.6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.018 / Rrim(I) all: 0.078 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6117 / CC1/2: 0.89 / Rpim(I) all: 0.232 / Rrim(I) all: 1.009 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N40 Resolution: 1.6→67.6 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.82 Å2 / Biso mean: 27.721 Å2 / Biso min: 12.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→67.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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