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- PDB-4ktj: Crystal structure of Mycobacterium tuberculosis CYP121 in complex... -

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Basic information

Entry
Database: PDB / ID: 4ktj
TitleCrystal structure of Mycobacterium tuberculosis CYP121 in complex with 4-(3-amino-1H-pyrazol-4-yl)phenol
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / P450 / cYY / C-C bond formation / Assumed cytosol
Function / homologyCytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE / 4-(3-amino-1H-pyrazol-4-yl)phenol / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHudson, S.A.
CitationJournal: Chemmedchem / Year: 2013
Title: Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121.
Authors: Hudson, S.A. / Surade, S. / Coyne, A.G. / McLean, K.J. / Leys, D. / Munro, A.W. / Abell, C.
History
DepositionMay 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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)44,1585
Polymers43,1751
Non-polymers9844
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.030, 78.030, 265.161
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-789-

HOH

21A-817-

HOH

31A-909-

HOH

41A-930-

HOH

51A-945-

HOH

61A-972-

HOH

71A-991-

HOH

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Components

#1: Protein Cytochrome P450 121


Mass: 43174.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2276, RVBD_2276 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: I6YD01, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-KTJ / 4-(3-amino-1H-pyrazol-4-yl)phenol


Mass: 175.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2M Ammonium sulfate, 0.1M Sodium cacodylate-HCl, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91731 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 1.35→35.69 Å / Num. all: 83209 / Num. obs: 83209 / % possible obs: 80.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Net I/σ(I): 7.4
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 12799 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.7.003refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.7.003phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N40

1n40


Resolution: 1.35→33.62 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.815 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19464 3611 5 %RANDOM
Rwork0.16502 ---
obs0.1665 79012 78.75 %-
all-79012 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.667 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 66 509 3551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0193182
X-RAY DIFFRACTIONr_bond_other_d0.0030.023093
X-RAY DIFFRACTIONr_angle_refined_deg2.6512.0114365
X-RAY DIFFRACTIONr_angle_other_deg1.723.0017108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72423.411129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19415516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3291527
X-RAY DIFFRACTIONr_chiral_restr0.1540.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213572
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 310 -
Rwork0.27 6154 -
obs--84.85 %

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