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Yorodumi- PDB-8a9p: Crystal structure of CYP142 from Mycobacterium tuberculosis in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a9p | ||||||
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Title | Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with a fragment | ||||||
Components | Steroid C26-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / CYP / P450 / cholesterol / Cyp142 / monooxygenase / cytochrome / tuberculosis / mycobacterium | ||||||
Function / homology | Function and homology information cholesterol 26-hydroxylase activity / cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / peptidoglycan-based cell wall / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Snee, M. / Katariya, M. / Levy, C. / Leys, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of CYP142 from Mycobacterium tuberculosis in complex with a fragment Authors: Snee, M. / Katariya, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a9p.cif.gz | 304.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a9p.ent.gz | 208.1 KB | Display | PDB format |
PDBx/mmJSON format | 8a9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a9p_validation.pdf.gz | 1020.3 KB | Display | wwPDB validaton report |
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Full document | 8a9p_full_validation.pdf.gz | 1021.4 KB | Display | |
Data in XML | 8a9p_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 8a9p_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a9p ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a9p | HTTPS FTP |
-Related structure data
Related structure data | 2xkrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44371.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: cyp142, cyp142A1, Rv3518c, MTV023.25c / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P9WPL5, cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] |
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-Non-polymers , 5 types, 338 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-ENK / ( | ||||
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-BR / | #6: 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: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M sodium Acetate pH4.5, 8% PEG 20,000 , 8% PEG 550MME, 0.25M KBr. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 4C / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→66.5 Å / Num. obs: 60601 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.412 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2955 / CC1/2: 0.705 / Rpim(I) all: 0.613 / % possible all: 98.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XKR Resolution: 1.63→42.56 Å / SU ML: 0.1999 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→42.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.3853043832 Å / Origin y: 45.3596311019 Å / Origin z: 82.3839715146 Å
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Refinement TLS group | Selection details: all |