+Open data
-Basic information
Entry | Database: PDB / ID: 6rq1 | ||||||
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Title | CYP121 in complex with 2-methyl dicyclotyrosine | ||||||
Components | Mycocyclosin synthase | ||||||
Keywords | OXIDOREDUCTASE / CYP121 / P450 / dicyclotyrosine derivatives / heme | ||||||
Function / homology | Function and homology information mycocyclosin synthase / cyclase activity / 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 / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity ...mycocyclosin synthase / cyclase activity / 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 / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Poddar, H. / Levy, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Structure-Activity Relationships of cyclo (l-Tyrosyl-l-tyrosine) Derivatives Binding to Mycobacterium tuberculosis CYP121: Iodinated Analogues Promote Shift to High-Spin Adduct. Authors: Rajput, S. / McLean, K.J. / Poddar, H. / Selvam, I.R. / Nagalingam, G. / Triccas, J.A. / Levy, C.W. / Munro, A.W. / Hutton, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rq1.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rq1.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rq1_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6rq1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6rq1_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 6rq1_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/6rq1 ftp://data.pdbj.org/pub/pdb/validation_reports/rq/6rq1 | HTTPS FTP |
-Related structure data
Related structure data | 6rq0C 6rq3C 6rq5C 6rq6C 6rq8C 6rq9C 6rqbC 6rqdC 6rqeC 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 / Fragment: Mycocyclosin synthase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, MT2336 / Variant: CDC 1551 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Variant (production host): HMS174(DE3) References: UniProt: P9WPP6, UniProt: P9WPP7*PLUS, mycocyclosin synthase |
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-Non-polymers , 5 types, 407 molecules
#2: Chemical | ChemComp-MES / | ||
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#3: Chemical | ChemComp-HEM / | ||
#4: Chemical | ChemComp-KE5 / ( | ||
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5 - 2.1 M Ammonium sulfate, 0.1 M MES / PH range: 5.5 - 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→65.2 Å / Num. obs: 77945 / % possible obs: 99.8 % / Redundancy: 12 % / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.49→1.5 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2502 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1N40 Resolution: 1.49→59.998 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.48 Å2 / Biso mean: 21.1037 Å2 / Biso min: 9.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→59.998 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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