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- PDB-5lie: Crystal structure of Mycobacterium tuberculosis CYP126A1 in compl... -

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Basic information

Entry
Database: PDB / ID: 5lie
TitleCrystal structure of Mycobacterium tuberculosis CYP126A1 in complex with imidazole
ComponentsPutative cytochrome P450 126
KeywordsOXIDOREDUCTASE / monoxygenase / cytochrome P450
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / steroid hydroxylase activity / cholesterol catabolic process / 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 / IMIDAZOLE / Putative cytochrome P450 126
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsLevy, C. / Munro, A.W. / Leys, D.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1.
Authors: Chenge, J.T. / Duyet, L.V. / Swami, S. / McLean, K.J. / Kavanagh, M.E. / Coyne, A.G. / Rigby, S.E. / Cheesman, M.R. / Girvan, H.M. / Levy, C.W. / Rupp, B. / von Kries, J.P. / Abell, C. / Leys, D. / Munro, A.W.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytochrome P450 126
B: Putative cytochrome P450 126
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3245
Polymers92,0222
Non-polymers1,3023
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-56 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.930, 70.050, 233.660
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 126 / CYP126A1


Mass: 46010.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp126, MT0802 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPN8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2 M sodium sulphate, 0.1 M Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.799→46.994 Å / Num. obs: 90448 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 13.4
Reflection shellHighest resolution: 1.799 Å / Rmerge(I) obs: 0.423

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Processing

Software
NameVersionClassification
PHENIX1.6_289refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXA

1oxa


Resolution: 1.799→46.994 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 18.05
RfactorNum. reflection% reflection
Rfree0.203 4530 5.01 %
Rwork0.1662 --
obs0.1681 90448 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 42.378 Å2 / ksol: 0.417 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8307 Å20 Å20 Å2
2--0.3668 Å2-0 Å2
3---1.4639 Å2
Refinement stepCycle: LAST / Resolution: 1.799→46.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6114 0 91 860 7065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166375
X-RAY DIFFRACTIONf_angle_d1.4448689
X-RAY DIFFRACTIONf_dihedral_angle_d14.7322325
X-RAY DIFFRACTIONf_chiral_restr0.1941
X-RAY DIFFRACTIONf_plane_restr0.0081142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.86330.23874490.17958427X-RAY DIFFRACTION99
1.8633-1.9380.21584330.17028541X-RAY DIFFRACTION100
1.938-2.02620.21384420.17268513X-RAY DIFFRACTION100
2.0262-2.1330.20114780.1658539X-RAY DIFFRACTION100
2.133-2.26660.19884420.16068583X-RAY DIFFRACTION100
2.2666-2.44160.22094340.15998548X-RAY DIFFRACTION100
2.4416-2.68730.2024420.15928655X-RAY DIFFRACTION100
2.6873-3.07610.20384390.16688642X-RAY DIFFRACTION100
3.0761-3.87530.19734820.15858703X-RAY DIFFRACTION100
3.8753-47.01040.1914890.1728767X-RAY DIFFRACTION97

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