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- PDB-4iq7: Substrate and reaction specificity of Mycobacterium tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 4iq7
TitleSubstrate and reaction specificity of Mycobacterium tuberculosis cytochrome P450 CYP121
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / protein-ligand complex / P450 fold / oxidase
Function / homology
Function and homology information


mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / oxidoreductase activity / iron ion binding ...mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / oxidoreductase activity / iron ion binding / heme binding / cytoplasm
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
Chem-1G9 / PROTOPORPHYRIN IX CONTAINING FE / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsFonvielle, M. / Ledu, M.H. / Lequin, O. / Lecoq, A. / Jacquet, M. / Thai, R. / Dubois, S. / Grach, G. / Gondry, M. / Belin, P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Substrate and Reaction Specificity of Mycobacterium tuberculosis Cytochrome P450 CYP121: INSIGHTS FROM BIOCHEMICAL STUDIES AND CRYSTAL STRUCTURES.
Authors: Fonvielle, M. / Le Du, M.H. / Lequin, O. / Lecoq, A. / Jacquet, M. / Thai, R. / Dubois, S. / Grach, G. / Gondry, M. / Belin, P.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5068
Polymers43,1751
Non-polymers1,3317
Water10,899605
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450 121
hetero molecules

A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,01116
Polymers86,3492
Non-polymers2,66214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6410 Å2
ΔGint-200 kcal/mol
Surface area32220 Å2
MethodPISA
3
A: Cytochrome P450 121
hetero molecules

A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,01116
Polymers86,3492
Non-polymers2,66214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area6870 Å2
ΔGint-200 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.890, 77.890, 263.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1065-

HOH

21A-1078-

HOH

31A-1088-

HOH

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Components

#1: Protein Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43174.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, Rv2276, MT2336, MTCY339.34c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A514, UniProt: P9WPP7*PLUS, 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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1G9 / (3S,6S)-3-(4-hydroxybenzyl)-6-methylpiperazine-2,5-dione


Mass: 234.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ammonium sulfate 2.2 M NaMes 0.1 M, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2010
RadiationMonochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 38439 / Num. obs: 37824 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.146
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.435 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
FFTmodel building
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→29.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1886 5 %RANDOM
Rwork0.15 ---
obs0.152 37702 --
all-39588 --
Displacement parametersBiso mean: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.3395 Å20 Å20 Å2
2---1.3395 Å20 Å2
3---2.679 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 85 605 3721
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013229HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994409HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1098SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes478HARMONIC5
X-RAY DIFFRACTIONt_it3229HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion14.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2158 130 4.48 %
Rwork0.189 2769 -
all0.1901 2899 -
Refinement TLS params.Method: refined / Origin x: 6.2345 Å / Origin y: 21.5895 Å / Origin z: -11.3723 Å
111213212223313233
T-0.0135 Å20.0103 Å20.0084 Å2--0.0655 Å2-0.0024 Å2--0.0117 Å2
L0.2663 °20.0037 °20.0403 °2-0.3239 °20.0236 °2--0.3332 °2
S0.0164 Å °0.0079 Å °0.0277 Å °0.0012 Å °0.0048 Å °-0.0331 Å °-0.088 Å °0.0223 Å °-0.0212 Å °
Refinement TLS groupSelection details: { A|* }

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