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- PDB-5li7: Crystal structure of Mycobacterium tuberculosis CYP126A1 in compl... -

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Basic information

Entry
Database: PDB / ID: 5li7
TitleCrystal structure of Mycobacterium tuberculosis CYP126A1 in complex with 1-(3-(1H-imidazol-1-yl)propyl)-3-((3s,5s,7s)-adamantan-1-yl)urea
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
1-(1-adamantyl)-3-(3-imidazol-1-ylpropyl)urea / PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450 126
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 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 1.2Jan 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)93,8606
Polymers92,0222
Non-polymers1,8384
Water17,979998
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-54 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.250, 69.910, 226.140
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


Mass: 46010.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (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-6XD / 1-(1-adamantyl)-3-(3-imidazol-1-ylpropyl)urea


Mass: 302.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 998 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium sulphate, 0.1 M Hepes pH 7.5 and 20% PEG 3350

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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: Jan 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.58→57.31 Å / Num. obs: 122489 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 20.1
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXA

1oxa


Resolution: 1.58→57.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.425 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20327 6486 5 %RANDOM
Rwork0.1701 ---
obs0.17176 122488 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.24 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.58→57.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 0 130 998 7009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0216279
X-RAY DIFFRACTIONr_bond_other_d0.0010.024297
X-RAY DIFFRACTIONr_angle_refined_deg2.0562.018581
X-RAY DIFFRACTIONr_angle_other_deg1.124310328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53522.185302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77415987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7011575
X-RAY DIFFRACTIONr_chiral_restr0.1390.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021365
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_it1.3331.53773
X-RAY DIFFRACTIONr_mcbond_other0.4431.51522
X-RAY DIFFRACTIONr_mcangle_it2.2626092
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.40432506
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3534.52485
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.581→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 493 -
Rwork0.26 8783 -
obs--100 %

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