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- PDB-3cxy: Crystal structure of the cytochrome P450 CYP121 P346L mutant from... -

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Basic information

Entry
Database: PDB / ID: 3cxy
TitleCrystal structure of the cytochrome P450 CYP121 P346L mutant from M. tuberculosis
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / Cytochrome P450 / CYP121 / Mycobacterium tuberculosis / Cytoplasm / 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 / carbon monoxide binding / 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 H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsLeys, D.
CitationJournal: TO BE PUBLISHED
Title: Characterization of active site structure in CYP121
Authors: McLean, K.J. / Carrol, P. / Lewis, D.G. / Dunford, A.J. / Seward, H.E. / Neeli, R. / Cole, S.T. / Leys, D. / Parish, T. / Munro, A.W.
History
DepositionApr 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2275
Polymers43,3221
Non-polymers9054
Water13,079726
1
A: Cytochrome P450 121
hetero molecules

A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,45310
Polymers86,6442
Non-polymers1,8098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area5770 Å2
ΔGint-145 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.714, 77.714, 265.046
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-1013-

HOH

21A-1060-

HOH

31A-1195-

HOH

41A-1501-

HOH

51A-1502-

HOH

61A-1503-

HOH

71A-1531-

HOH

Detailsmonomer in the AU, oligomeric organisation in solution is unclear

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Components

#1: Protein Cytochrome P450 121 / P450 MT2


Mass: 43321.906 Da / Num. of mol.: 1 / Mutation: P346L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp121 / 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.: 3 / 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.: 726 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium sulphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 78019 / Num. obs: 78019 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1N40

1n40


Resolution: 1.45→25.4 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.151 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18598 4114 5 %RANDOM
Rwork0.15241 ---
all0.15408 78019 --
obs0.15408 78019 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.583 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 71 726 3864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223210
X-RAY DIFFRACTIONr_bond_other_d0.0010.023078
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.0464405
X-RAY DIFFRACTIONr_angle_other_deg1.86837122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1935392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.57423.206131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19915532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3651529
X-RAY DIFFRACTIONr_chiral_restr0.0810.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
X-RAY DIFFRACTIONr_nbd_refined0.2240.2752
X-RAY DIFFRACTIONr_nbd_other0.1870.23298
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21597
X-RAY DIFFRACTIONr_nbtor_other0.0850.21841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4280.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1721.52133
X-RAY DIFFRACTIONr_mcbond_other0.5231.5787
X-RAY DIFFRACTIONr_mcangle_it1.59323247
X-RAY DIFFRACTIONr_scbond_it2.20331309
X-RAY DIFFRACTIONr_scangle_it3.1334.51155
X-RAY DIFFRACTIONr_rigid_bond_restr1.14936863
X-RAY DIFFRACTIONr_sphericity_free5.4643726
X-RAY DIFFRACTIONr_sphericity_bonded2.71936216
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 301 -
Rwork0.225 5375 -
obs--100 %

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