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- PDB-6upg: Crystal structure of Mycobacterium tuberculosis CYP121 in complex... -

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Basic information

Entry
Database: PDB / ID: 6upg
TitleCrystal structure of Mycobacterium tuberculosis CYP121 in complex with cYF-4-OMe
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / analog / C-C / unusual / P450
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 / 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-KEQ / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.393 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: 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
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)44,1323
Polymers43,1751
Non-polymers9572
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-27 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.460, 77.460, 262.588
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-559-

HOH

21A-850-

HOH

31A-882-

HOH

41A-915-

HOH

51A-965-

HOH

61A-1040-

HOH

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Components

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


Mass: 43174.668 Da / Num. of mol.: 1 / Mutation: 0
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


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


Mass: 340.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 279.2 K / Method: vapor diffusion, hanging drop / Details: 1.95 M ammonium sulfate, 100 mM MES, pH 5.1-5.3 / PH range: 5.1-5.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 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: 1.39→50 Å / Num. obs: 93972 / % possible obs: 99.2 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.029 / Rrim(I) all: 0.132 / Χ2: 1.143 / Net I/σ(I): 4.8 / Num. measured all: 1898703
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.39-1.4119.30.38939610.950.0870.3990.58385.5
1.41-1.4420.50.36546240.9560.080.3740.62799.7
1.44-1.4720.40.33546420.960.0740.3430.69499.8
1.47-1.520.20.30946280.9710.0680.3170.74499.7
1.5-1.53200.2946270.9740.0650.2980.80599.7
1.53-1.5719.20.26746630.9770.0610.2740.82499.8
1.57-1.619.10.24846510.9790.0570.2540.84799.8
1.6-1.6520.60.2346820.9830.050.2360.90499.8
1.65-1.720.50.21946500.9820.0480.2250.96199.9
1.7-1.7520.30.20846810.9860.0460.2141.00599.9
1.75-1.8119.90.19747040.9870.0440.2021.102100
1.81-1.8918.60.19346970.9860.0450.1981.23799.9
1.89-1.9720.90.18347090.990.040.1871.396100
1.97-2.0820.90.17547160.9910.0380.1791.56299.9
2.08-2.2120.70.16247610.9910.0360.1661.64999.9
2.21-2.3819.60.1547310.9930.0340.1541.66899.9
2.38-2.6221.10.14148020.9940.0310.1441.585100
2.62-2.9921.40.1348560.9950.0280.1331.552100
2.99-3.7720.50.11549130.9950.0260.1181.55899.9
3.77-5020.40.09752740.9960.0220.0991.25199.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WP2

5wp2


Resolution: 1.393→46.919 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.1947 1999 2.13 %
Rwork0.1855 --
obs0.1857 93826 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.42 Å2 / Biso mean: 18.3731 Å2 / Biso min: 8.31 Å2
Refinement stepCycle: final / Resolution: 1.393→46.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 68 545 3623
Biso mean--14.22 25.99 -
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 (%)
1.393-1.42770.22751380.2152634598
1.4277-1.46630.23831410.20826442100
1.4663-1.50950.20541400.20326436100
1.5095-1.55820.20751390.1966443100
1.5582-1.61390.21241410.1926502100
1.6139-1.67850.18751410.19396450100
1.6785-1.75490.21331420.19036480100
1.7549-1.84750.20741410.18866533100
1.8475-1.96320.22081420.18456507100
1.9632-2.11480.18551430.18086561100
2.1148-2.32760.19351440.17936608100
2.3276-2.66440.17771450.18666646100
2.6644-3.35670.19061470.1876750100
3.3567-46.9190.1891550.1787124100

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