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- PDB-3g5f: Crystallographic analysis of cytochrome P450 cyp121 -

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Basic information

Entry
Database: PDB / ID: 3g5f
TitleCrystallographic analysis of cytochrome P450 cyp121
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / cytochrome / tuberculosis / cyp121 / P450 / Heme / Iron / Metal-binding / Monooxygenase
Function / homology
Function and homology information


mycocyclosin synthase / cyclase activity / 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 / cholest-4-en-3-one 26-monooxygenase activity / carbon monoxide binding / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / oxidoreductase activity / iron ion binding ...mycocyclosin synthase / cyclase activity / 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 / cholest-4-en-3-one 26-monooxygenase activity / carbon monoxide binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBelin, P. / Le Du, M.H. / Gondry, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Identification and structural basis of the reaction catalyzed by CYP121, an essential cytochrome P450 in Mycobacterium tuberculosis.
Authors: Belin, P. / Le Du, M.H. / Fielding, A. / Lequin, O. / Jacquet, M. / Charbonnier, J.B. / Lecoq, A. / Thai, R. / Courcon, M. / Masson, C. / Dugave, C. / Genet, R. / Pernodet, J.L. / Gondry, M.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Nov 1, 2023Group: 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_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)44,3076
Polymers43,3061
Non-polymers1,0015
Water13,944774
1


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

A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,61312
Polymers86,6122
Non-polymers2,00110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area6470 Å2
ΔGint-181 kcal/mol
Surface area31590 Å2
MethodPISA
3
A: Cytochrome P450 121
hetero molecules

A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,61312
Polymers86,6122
Non-polymers2,00110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5860 Å2
ΔGint-173 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.373, 77.373, 264.050
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-511-

HOH

21A-623-

HOH

31A-753-

HOH

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Components

#1: Protein Cytochrome P450 121 / P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 774 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 277 K / pH: 6.5
Details: Ammonium sulfate, seating drop, vapor diffusion, pH 6.5, temperature 277K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.4→67.27 Å / Num. all: 93031 / Num. obs: 93031 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 12.2 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.3 / Num. unique all: 13293 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N40

1n40


Resolution: 1.4→38.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.653 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19024 4676 5 %RANDOM
Rwork0.1588 ---
obs0.16039 88208 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 63 774 3868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223191
X-RAY DIFFRACTIONr_angle_refined_deg1.4112.0344354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.72223.309136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3261530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022414
X-RAY DIFFRACTIONr_nbd_refined0.2230.21678
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2598
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.269
X-RAY DIFFRACTIONr_mcbond_it1.2691.52032
X-RAY DIFFRACTIONr_mcangle_it1.79723198
X-RAY DIFFRACTIONr_scbond_it2.58431288
X-RAY DIFFRACTIONr_scangle_it3.7194.51154
X-RAY DIFFRACTIONr_rigid_bond_restr1.40933320
X-RAY DIFFRACTIONr_sphericity_free4.7873774
X-RAY DIFFRACTIONr_sphericity_bonded4.28433124
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 331 -
Rwork0.175 6403 -
obs--99.75 %

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