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- PDB-2ij5: Crystal structure of cytochrome P450 CYP121, P212121 space group -

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Basic information

Entry
Database: PDB / ID: 2ij5
TitleCrystal structure of cytochrome P450 CYP121, P212121 space group
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / tuberculosis / CYP121 / cytochrome P450 / azole ligation / fluconazole
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRoujeinikova, A. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the Mycobacterium tuberculosis P450 CYP121-fluconazole complex reveals new azole drug-P450 binding mode.
Authors: Seward, H.E. / Roujeinikova, A. / McLean, K.J. / Munro, A.W. / Leys, D.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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
B: Cytochrome P450 121
C: Cytochrome P450 121
D: Cytochrome P450 121
E: Cytochrome P450 121
F: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,11018
Polymers259,8356
Non-polymers4,27512
Water47,4522634
1
A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0183
Polymers43,3061
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0183
Polymers43,3061
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0183
Polymers43,3061
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0183
Polymers43,3061
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0183
Polymers43,3061
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0183
Polymers43,3061
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.627, 129.758, 323.757
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
Cytochrome P450 121 / P450 MT2


Mass: 43305.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121
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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2634 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350 and 0.2M NaSCN, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 314231 / Num. obs: 314231 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N40

1n40


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.712 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21022 16692 5 %RANDOM
Rwork0.16465 ---
all0.16693 314231 --
obs0.16693 314231 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17799 0 288 2634 20721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02218498
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217555
X-RAY DIFFRACTIONr_angle_refined_deg1.5342.02925308
X-RAY DIFFRACTIONr_angle_other_deg0.913340545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3652336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12123.338746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.325152925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.59315160
X-RAY DIFFRACTIONr_chiral_restr0.0920.22914
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023549
X-RAY DIFFRACTIONr_nbd_refined0.2230.24071
X-RAY DIFFRACTIONr_nbd_other0.190.218047
X-RAY DIFFRACTIONr_nbtor_refined0.1780.29352
X-RAY DIFFRACTIONr_nbtor_other0.0850.210127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21732
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1520.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.2254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.2101
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4251.512574
X-RAY DIFFRACTIONr_mcbond_other0.661.54690
X-RAY DIFFRACTIONr_mcangle_it1.913218918
X-RAY DIFFRACTIONr_scbond_it2.93537223
X-RAY DIFFRACTIONr_scangle_it3.9634.56378
X-RAY DIFFRACTIONr_rigid_bond_restr1.922339338
X-RAY DIFFRACTIONr_sphericity_free7.76832635
X-RAY DIFFRACTIONr_sphericity_bonded3.06335641
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 1172 -
Rwork0.206 21444 -
obs--100 %

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