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- PDB-2xn8: X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS ... -

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Basic information

Entry
Database: PDB / ID: 2xn8
TitleX-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125
ComponentsPUTATIVE CYTOCHROME P450 125
KeywordsOXIDOREDUCTASE / CHOLESTEROL DEGRADATION / REVERSE TYPE I INHIBITOR / MONOOXYGENASE
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 / biological process involved in interaction with host / steroid hydroxylase activity / cholesterol catabolic process / 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 / Steroid C26-monooxygenase / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsOuellet, H. / Kells, P.M. / Ortiz de Montellano, P.R. / Podust, L.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Reverse Type I Inhibitor of Mycobacteriumtuberculosis Cyp125A1.
Authors: Ouellet, H. / Kells, P.M. / Ortiz de Montellano, P.R. / Podust, L.M.
History
DepositionJul 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 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

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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)48,1753
Polymers47,4621
Non-polymers7132
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.365, 76.316, 90.357
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 125 / CYP125A1


Mass: 47462.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-433 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. 6XHIS TAG IS ENGINEERED AT THE N-TERMINUS
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS 377
Sequence detailsFIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L ARE ENGINEERED. 6XHIS TAG ...FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L ARE ENGINEERED. 6XHIS TAG IS ENGINEERED AT THE N-TERMINUS

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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: 1.95 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.5
Details: 2.0M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5, 4 DEG. CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.64→15.53 Å / Num. obs: 46349 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 6.1 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5L

2x5l


Resolution: 1.64→58.3 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.989 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 234-235 AND 248-249 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.21003 2333 5 %RANDOM
Rwork0.14059 ---
obs0.14406 43947 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.975 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.79 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.64→58.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 48 464 3699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223380
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9774615
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6423.804163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44615520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4271524
X-RAY DIFFRACTIONr_chiral_restr0.150.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212671
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_it2.021.52073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04423327
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.86231307
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.7434.51285
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.57533380
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 164 -
Rwork0.252 2887 -
obs--90.27 %

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