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- PDB-1n4g: Structure of CYP121, a Mycobacterial P450, in Complex with Iodopy... -

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Basic information

Entry
Database: PDB / ID: 1n4g
TitleStructure of CYP121, a Mycobacterial P450, in Complex with Iodopyrazole
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / P450 fold / iodopyrazole complex / heme binding / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / 4-IODOPYRAZOLE / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 31, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1163
Polymers43,3061
Non-polymers8102
Water9,710539
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.717, 78.717, 268.240
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-732-

HOH

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Components

#1: Protein Cytochrome P450 121 / P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1 / Fragment: P450 CYP 121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: CYP121 OR RV2276 OR MT2336 OR MTCY339.34C / Plasmid: PET11A / 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-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3IN2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.42 Å3/Da / Density % sol: 48.87 %
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 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: 1.8→20 Å / Num. all: 44862 / Num. obs: 44862 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.84 Å / % possible all: 90.6
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % possible obs: 95.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N40

1n40


Resolution: 1.8→9.98 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.545 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21735 2284 5.1 %RANDOM
Rwork0.20511 ---
all0.20573 42578 --
obs0.20573 42578 100 %-
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: 14.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→9.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 49 539 3534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223057
X-RAY DIFFRACTIONr_bond_other_d0.0040.022900
X-RAY DIFFRACTIONr_angle_refined_deg1.8652.0154186
X-RAY DIFFRACTIONr_angle_other_deg1.60336686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315469
X-RAY DIFFRACTIONr_chiral_restr0.110.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023411
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02591
X-RAY DIFFRACTIONr_nbd_refined0.2150.2541
X-RAY DIFFRACTIONr_nbd_other0.2680.22632
X-RAY DIFFRACTIONr_nbtor_other0.0720.21368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8211.51960
X-RAY DIFFRACTIONr_mcangle_it1.43723146
X-RAY DIFFRACTIONr_scbond_it2.60531097
X-RAY DIFFRACTIONr_scangle_it4.24.51040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 163 -
Rwork0.22 2800 -
obs-2751 90.6 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.35

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