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- PDB-2x5w: X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP... -

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Basic information

Entry
Database: PDB / ID: 2x5w
TitleX-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with substrate cholest-4-en-3-one
ComponentsPUTATIVE CYTOCHROME P450 125
KeywordsOXIDOREDUCTASE / CHOLESTEROL DEGRADATION / METAL-BINDING
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / cholesterol catabolic process / biological process involved in interaction with host / steroid hydroxylase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE / Steroid C26-monooxygenase / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsOuellet, H. / Guan, S. / Johnston, J.B. / Chow, E.D. / Kells, P.M. / Burlingame, A.L. / Cox, J.S. / Podust, L.M. / Ortiz de Montellano, P.R.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Mycobacterium Tuberculosis Cyp125A1, a Steroid C27 Monooxygenase that Detoxifies Intracellularly Generated Cholest-4-En-3-One.
Authors: Ouellet, H. / Guan, S. / Johnston, J.B. / Chow, E.D. / Kells, P.M. / Burlingame, A.L. / Cox, J.S. / Podust, L.M. / Ortiz de Montellano, P.R.
History
DepositionFeb 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...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 / 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
Revision 1.6Sep 2, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE CYTOCHROME P450 125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6115
Polymers49,4521
Non-polymers1,1594
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.666, 75.977, 79.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PUTATIVE CYTOCHROME P450 125 / CYP125A1


Mass: 49451.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): HMS174
References: UniProt: P63709, UniProt: P9WPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K2B / (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE


Mass: 384.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growTemperature: 277 K / pH: 5.5
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M BIS- TRIS, PH 5.5, 25% PEG 3350, 4 DEGREE C.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.58→75.98 Å / Num. obs: 61386 / % possible obs: 99.3 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IVY

3ivy


Resolution: 1.58→79.59 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.286 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3098 5 %RANDOM
Rwork0.146 ---
obs0.149 58287 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.58→79.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 80 438 3714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9884784
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68624.171175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41715543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2161525
X-RAY DIFFRACTIONr_chiral_restr0.1440.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212790
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2631.52115
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.23323410
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8931382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4134.51374
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.65833497
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 195 -
Rwork0.327 4003 -
obs--93.35 %

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