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- PDB-4tri: X-ray crystal structure of CYP142A2 from Mycobacterium smegmatis,... -

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Basic information

Entry
Database: PDB / ID: 4tri
TitleX-ray crystal structure of CYP142A2 from Mycobacterium smegmatis, complexed with cholesterol sulfate.
ComponentsP450 heme-thiolate protein
KeywordsOXIDOREDUCTASE / Cytochrome P450 / cholesterol sulfate / ligand bound
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / cholesterol catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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
CHOLEST-5-EN-3-YL HYDROGEN SULFATE / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMadrona, Y. / Ortiz de Montellano, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Cholesterol ester oxidation by mycobacterial cytochrome p450.
Authors: Frank, D.J. / Madrona, Y. / Ortiz de Montellano, P.R.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P450 heme-thiolate protein
B: P450 heme-thiolate protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9118
Polymers91,5602
Non-polymers2,3516
Water12,935718
1
A: P450 heme-thiolate protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9554
Polymers45,7801
Non-polymers1,1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P450 heme-thiolate protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9554
Polymers45,7801
Non-polymers1,1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.455, 96.140, 145.888
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 P450 heme-thiolate protein


Mass: 45780.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5918 / Plasmid: pCWori / Details (production host): c-terminal His tag / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4Q6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-C3S / CHOLEST-5-EN-3-YL HYDROGEN SULFATE / CHOLESTEROL-SULFATE / Cholesterol sulfate


Mass: 466.717 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20-28% PEG 3350, 50mM NaCl, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: R-AXIS IV, In-house data collection
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2014
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 55973 / Num. obs: 53177 / % possible obs: 94.15 % / Observed criterion σ(F): 0.02 / Redundancy: 3.5 % / Rsym value: 0.077 / Net I/σ(I): 16.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2→29.055 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 2788 4.98 %Random selection
Rwork0.1626 ---
obs0.1651 55965 94.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 162 718 7155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076610
X-RAY DIFFRACTIONf_angle_d1.1659009
X-RAY DIFFRACTIONf_dihedral_angle_d13.3122463
X-RAY DIFFRACTIONf_chiral_restr0.043994
X-RAY DIFFRACTIONf_plane_restr0.0051177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.03140.28261230.21242366X-RAY DIFFRACTION85
2.0314-2.06830.32991310.21522567X-RAY DIFFRACTION93
2.0683-2.10810.26491170.19712633X-RAY DIFFRACTION93
2.1081-2.15110.28931100.1892610X-RAY DIFFRACTION93
2.1511-2.19790.26391450.18152613X-RAY DIFFRACTION93
2.1979-2.2490.22581470.17852571X-RAY DIFFRACTION94
2.249-2.30520.26971680.17552588X-RAY DIFFRACTION94
2.3052-2.36750.23571500.16342649X-RAY DIFFRACTION94
2.3675-2.43710.26031210.17242653X-RAY DIFFRACTION94
2.4371-2.51570.26881490.18252623X-RAY DIFFRACTION94
2.5157-2.60560.23671540.17152647X-RAY DIFFRACTION95
2.6056-2.70980.24861200.17812675X-RAY DIFFRACTION95
2.7098-2.83310.22461580.17512693X-RAY DIFFRACTION95
2.8331-2.98230.21961350.17762676X-RAY DIFFRACTION95
2.9823-3.16890.22561440.17212698X-RAY DIFFRACTION96
3.1689-3.41330.21681410.17292722X-RAY DIFFRACTION95
3.4133-3.75610.21621470.15042684X-RAY DIFFRACTION95
3.7561-4.29810.17041450.13722777X-RAY DIFFRACTION96
4.2981-5.40950.13541520.12872804X-RAY DIFFRACTION97
5.4095-29.05850.18551310.15242928X-RAY DIFFRACTION96

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