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- PDB-6upi: Crystal structure of Mycobacterium tuberculosis CYP121 bound with... -

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Basic information

Entry
Database: PDB / ID: 6upi
TitleCrystal structure of Mycobacterium tuberculosis CYP121 bound with a hydroxylated intermediate of cYF-4-OMe
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / intermediate / complex / P450 / hydroxylation
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 / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / oxidoreductase activity ...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 / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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 / Chem-QFD / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.808 Å
AuthorsNguyen, R.C.D. / Yang, Y. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: Acs Catalysis / Year: 2020
Title: Substrate-Assisted Hydroxylation and O-Demethylation in the Peroxidase-like Cytochrome P450 Enzyme CYP121
Authors: Nguyen, R.C. / Yang, Y. / Davis, I. / Liu, A.
History
DepositionOct 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1483
Polymers43,1751
Non-polymers9732
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-27 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.370, 77.370, 261.973
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

21A-750-

HOH

31A-814-

HOH

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Components

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43174.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, MT2336 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WPP6, UniProt: P9WPP7*PLUS, mycocyclosin synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-QFD / (3S,6S)-3-{[4-(hydroxymethoxy)phenyl]methyl}-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione


Mass: 356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 279.2 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.95 M ammonium sulfate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 14, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.808→46.836 Å / Num. obs: 42901 / % possible obs: 98.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.119 / Χ2: 1.054 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.81-1.847.20.96920770.453197.7
1.84-1.877.20.83520570.47197.6
1.87-1.917.20.65820830.502198.1
1.91-1.957.20.57120900.529197.8
1.95-1.997.20.47620840.544197.9
1.99-2.047.10.39821180.57198.1
2.04-2.097.20.34220800.59198
2.09-2.157.10.29221050.648198.3
2.15-2.217.10.26121100.698198.5
2.21-2.2870.23621260.776198.2
2.28-2.367.10.20121120.783198.6
2.36-2.4670.17921290.866198.8
2.46-2.576.90.16621300.968198.3
2.57-2.770.1521521.069198.7
2.7-2.876.80.1321611.279198.6
2.87-3.096.70.11321811.481198.8
3.09-3.416.60.09221741.861198.6
3.41-3.96.40.08322102.394198.1
3.9-4.916.60.07522492.723198.2
4.91-506.20.06224732.063198.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WP2

5wp2


Resolution: 1.808→46.836 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.2245 2000 4.67 %
Rwork0.1846 --
obs0.1865 42865 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.44 Å2 / Biso mean: 24.4628 Å2 / Biso min: 12.66 Å2
Refinement stepCycle: final / Resolution: 1.808→46.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 94 335 3435
Biso mean--20.89 30.3 -
Num. residues----395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8084-1.85360.26411370.2397279197
1.8536-1.90380.25781380.2172282398
1.9038-1.95980.23411390.205284698
1.9598-2.0230.25451400.1906286298
2.023-2.09530.23661400.1876286898
2.0953-2.17920.23591400.1871286099
2.1792-2.27840.21271420.1802289298
2.2784-2.39850.24341410.1866288499
2.3985-2.54880.22041420.1949290299
2.5488-2.74560.23211440.1982293599
2.7456-3.02180.24431430.1959294299
3.0218-3.4590.23091470.1837297799
3.459-4.35740.17121480.1622302799
4.3574-46.8360.23871590.1775325699

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