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- PDB-2xkr: Crystal Structure of Mycobacterium tuberculosis CYP142: A novel c... -

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Basic information

Entry
Database: PDB / ID: 2xkr
TitleCrystal Structure of Mycobacterium tuberculosis CYP142: A novel cholesterol oxidase
ComponentsPUTATIVE CYTOCHROME P450 142
KeywordsOXIDOREDUCTASE
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 / cholesterol catabolic process / cell wall / steroid hydroxylase activity / : / peptidoglycan-based cell wall / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsDriscoll, M. / McLean, K.J. / Levy, C.W. / Lafite, P. / Mast, N. / Pikuleva, I.A. / Rigby, S.E.J. / Leys, D. / Munro, A.W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and Biochemical Characterization of Mycobacterium Tuberculosis Cyp142: Evidence for Multiple Cholesterol 27-Hydroxylase Activities in a Human Pathogen.
Authors: Driscoll, M.D. / Mclean, K.J. / Levy, C.W. / Mast, N. / Pikuleva, I.A. / Lafite, P. / Rigby, S.E.J. / Leys, D. / Munro, A.W.
History
DepositionJul 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE CYTOCHROME P450 142
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2563
Polymers44,4451
Non-polymers8112
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.310, 65.460, 129.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE CYTOCHROME P450 142 / CYP142


Mass: 44445.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: POLYETHYLENE GLYCOL BOUND TO HEME IRON / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: INSTITUT PASTEUR / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: O53563, UniProt: P9WPL5*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 % / Description: NONE
Crystal growpH: 7.5
Details: 10% PEG 550MME WITH 100 MM POTASSIUM THIOCYANATE AND 0.1 M SODIUM ACETATE AT A PH RANGE OF 5.0-6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.6→40.2 Å / Num. obs: 62547 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 16.47 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.1 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WM4

2wm4


Resolution: 1.601→40.164 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 3169 5.1 %
Rwork0.168 --
obs0.1694 62544 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.638 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.2708 Å20 Å20 Å2
2--1.9205 Å20 Å2
3----2.1913 Å2
Refinement stepCycle: LAST / Resolution: 1.601→40.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 50 510 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053180
X-RAY DIFFRACTIONf_angle_d1.0324334
X-RAY DIFFRACTIONf_dihedral_angle_d12.631177
X-RAY DIFFRACTIONf_chiral_restr0.067482
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.62490.25031220.20672463X-RAY DIFFRACTION97
1.6249-1.65030.22661430.19452536X-RAY DIFFRACTION100
1.6503-1.67740.23261420.18532570X-RAY DIFFRACTION100
1.6774-1.70630.23011390.18172524X-RAY DIFFRACTION100
1.7063-1.73730.20261350.18042570X-RAY DIFFRACTION100
1.7373-1.77070.18271300.17722552X-RAY DIFFRACTION100
1.7707-1.80690.22851480.17152553X-RAY DIFFRACTION100
1.8069-1.84620.21441250.17462580X-RAY DIFFRACTION100
1.8462-1.88910.21231270.16342544X-RAY DIFFRACTION100
1.8891-1.93630.19951510.16762557X-RAY DIFFRACTION100
1.9363-1.98870.1941390.1622594X-RAY DIFFRACTION100
1.9887-2.04720.18931390.16292581X-RAY DIFFRACTION100
2.0472-2.11330.19461410.15712524X-RAY DIFFRACTION100
2.1133-2.18880.16291220.15332604X-RAY DIFFRACTION100
2.1888-2.27640.19011500.15462552X-RAY DIFFRACTION100
2.2764-2.380.18621330.162599X-RAY DIFFRACTION100
2.38-2.50550.18791280.16382611X-RAY DIFFRACTION100
2.5055-2.66250.20691350.16862586X-RAY DIFFRACTION100
2.6625-2.8680.18871260.17372622X-RAY DIFFRACTION100
2.868-3.15650.23371500.18172609X-RAY DIFFRACTION100
3.1565-3.6130.19171500.16662622X-RAY DIFFRACTION100
3.613-4.5510.16291580.14192642X-RAY DIFFRACTION100
4.551-40.17640.17511360.17242780X-RAY DIFFRACTION99

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