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- PDB-1n40: Atomic structure of CYP121, a mycobacterial P450 -

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Basic information

Entry
Database: PDB / ID: 1n40
TitleAtomic structure of CYP121, a mycobacterial P450
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / heme binding / oxygen binding / P450 fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / cholest-4-en-3-one 26-monooxygenase activity / carbon monoxide binding / cholesterol catabolic process / steroid hydroxylase activity / 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 / cholest-4-en-3-one 26-monooxygenase activity / carbon monoxide binding / cholesterol catabolic process / steroid hydroxylase activity / 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 / OXYGEN MOLECULE / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.06 Å
AuthorsLeys, D. / Mowat, C.G. / McLean, K.J. / Richmond, A. / Chapman, S.K. / Walkinshaw, M.D. / Munro, A.W. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450.
Authors: Leys, D. / Mowat, C.G. / McLean, K.J. / Richmond, A. / Chapman, S.K. / Walkinshaw, M.D. / Munro, A.W.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2436
Polymers43,3061
Non-polymers9375
Water14,268792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.184, 77.184, 263.829
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-995-

HOH

21A-1310-

HOH

31A-1349-

HOH

41A-1600-

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) / Gene: CYP121 OR RV2276 OR MT2336 OR 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 792 / 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: 2.04 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: ammonium sulphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Mowat, C.G., (2002) Acta Crystallogr., D58, 704.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium MES1reservoirpH5.0-6.0
21.75-2.50 Mammonium sulfate1reservoir
310 mg/mlprotein1drop
450 mMTris-HCl1droppH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2002
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.06→10 Å / Num. all: 209932 / Num. obs: 176158 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.5
Reflection shellResolution: 1.06→1.088 Å / % possible all: 63.8
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 185472

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.06→10 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.294 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15309 9314 5 %RANDOM
Rwork0.13266 ---
all0.1337 176158 --
obs0.1337 176158 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.347 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: 1.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 103 792 3976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223210
X-RAY DIFFRACTIONr_bond_other_d0.0020.023076
X-RAY DIFFRACTIONr_angle_refined_deg1.9432.024398
X-RAY DIFFRACTIONr_angle_other_deg2.44837124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415536
X-RAY DIFFRACTIONr_chiral_restr0.2490.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023496
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02609
X-RAY DIFFRACTIONr_nbd_refined0.2310.21147
X-RAY DIFFRACTIONr_nbd_other0.280.23824
X-RAY DIFFRACTIONr_nbtor_other0.170.22871
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2482
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.271
X-RAY DIFFRACTIONr_mcbond_it1.5711.52000
X-RAY DIFFRACTIONr_mcangle_it2.24823267
X-RAY DIFFRACTIONr_scbond_it2.81531210
X-RAY DIFFRACTIONr_scangle_it3.8994.51130
X-RAY DIFFRACTIONr_rigid_bond_restr1.57623210
X-RAY DIFFRACTIONr_sphericity_free7.4592792
X-RAY DIFFRACTIONr_sphericity_bonded4.84223139
LS refinement shellResolution: 1.06→1.088 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 505 -
Rwork0.3 9389 -
obs-9389 63.9 %
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.153 / Rfactor Rwork: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.94
LS refinement shell
*PLUS
Rfactor Rwork: 0.3

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