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- PDB-8amo: Crystal structure of M. tuberculosis CYP143 -

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Basic information

Entry
Database: PDB / ID: 8amo
TitleCrystal structure of M. tuberculosis CYP143
ComponentsPutative cytochrome P450 143
KeywordsOXIDOREDUCTASE / M. tuberculosis / cytochrome P450 / rv1785c
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 143
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBukhdruker, S. / Varaksa, T. / Grudo, A. / Marin, E. / Kapranov, I. / Shevtsov, M. / Gilep, A. / Strushkevich, N. / Borshchevskiy, V.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Ministry of Science and Higher Education of the Russian Federation122030100168-2 Russian Federation
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450.
Authors: Gilep, A. / Varaksa, T. / Bukhdruker, S. / Kavaleuski, A. / Ryzhykau, Y. / Smolskaya, S. / Sushko, T. / Tsumoto, K. / Grabovec, I. / Kapranov, I. / Okhrimenko, I. / Marin, E. / Shevtsov, M. ...Authors: Gilep, A. / Varaksa, T. / Bukhdruker, S. / Kavaleuski, A. / Ryzhykau, Y. / Smolskaya, S. / Sushko, T. / Tsumoto, K. / Grabovec, I. / Kapranov, I. / Okhrimenko, I. / Marin, E. / Shevtsov, M. / Mishin, A. / Kovalev, K. / Kuklin, A. / Gordeliy, V. / Kaluzhskiy, L. / Gnedenko, O. / Yablokov, E. / Ivanov, A. / Borshchevskiy, V. / Strushkevich, N.
History
DepositionAug 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cytochrome P450 143
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3506
Polymers44,4221
Non-polymers9285
Water8,899494
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-33 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.210, 48.530, 54.150
Angle α, β, γ (deg.)111.652, 99.502, 109.340
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Putative cytochrome P450 143


Mass: 44422.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp143, Rv1785c, MTV049.07c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPL3, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M NaCl, 0.1 M BisTris, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.4→27.78 Å / Num. obs: 62494 / % possible obs: 88.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 17.76 Å2 / CC1/2: 1 / Rrim(I) all: 0.068 / Net I/σ(I): 14.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.447.40.1945000.2439.76886.6
1.44-1.487.60.4845530.4634.22489.6
1.48-1.527.60.8844350.7042.29689.4
1.52-1.577.51.3942220.81.50788.4
1.57-1.627.52.0640290.8881.01686.8
1.62-1.677.43.0436970.940.66882.7
1.67-1.747.64.3139700.9570.48591.6
1.74-1.817.55.8438100.9740.35390.9
1.81-1.897.68.6635940.9840.23890.1
1.89-1.987.611.8333490.9910.17388.6
1.98-2.097.515.8429680.9950.12281.2
2.09-2.217.621.2231600.9970.08991.6
2.21-2.377.525.6130000.9980.07193.2
2.37-2.567.630.1227810.9980.06192.1
2.56-2.87.433.3124670.9980.05689.4
2.8-3.137.338.8620890.9990.04683.9
3.13-3.617.446.4921150.9990.03795.4
3.61-4.437.551.7117540.9990.03293.1
4.43-6.267.552.412270.9990.03185.7
6.26-27.787.755.8977410.02597.5

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
MoRDaphasing
ARP/wARPmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DXY

4dxy


Resolution: 1.4→27.78 Å / SU ML: 0.1979 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 26.2632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1995 2658 4.97 %
Rwork0.1695 50841 -
obs0.171 53499 76.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.86 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 62 494 3527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633486
X-RAY DIFFRACTIONf_angle_d0.87474808
X-RAY DIFFRACTIONf_chiral_restr0.0691519
X-RAY DIFFRACTIONf_plane_restr0.0106644
X-RAY DIFFRACTIONf_dihedral_angle_d18.74391319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.4402610.40371159X-RAY DIFFRACTION32.84
1.43-1.450.4899710.35761335X-RAY DIFFRACTION38.05
1.45-1.480.3537770.34121486X-RAY DIFFRACTION42.92
1.48-1.510.3893900.32911707X-RAY DIFFRACTION48.38
1.51-1.550.37041070.31382023X-RAY DIFFRACTION57.74
1.55-1.590.34721220.31212470X-RAY DIFFRACTION71.07
1.59-1.630.33091530.29262924X-RAY DIFFRACTION82.74
1.63-1.680.31681520.25422951X-RAY DIFFRACTION83.35
1.68-1.730.23951730.243190X-RAY DIFFRACTION91.89
1.73-1.80.26691670.23553229X-RAY DIFFRACTION91.49
1.8-1.870.22321560.19613187X-RAY DIFFRACTION90.5
1.87-1.950.22251590.17193135X-RAY DIFFRACTION89.17
1.95-2.060.22831600.16652963X-RAY DIFFRACTION85.05
2.06-2.180.20261660.16043060X-RAY DIFFRACTION87.1
2.18-2.350.20781760.15293266X-RAY DIFFRACTION93.41
2.35-2.590.1871660.15053222X-RAY DIFFRACTION92.24
2.59-2.960.16441560.16273031X-RAY DIFFRACTION86.14
2.96-3.730.15871760.13633288X-RAY DIFFRACTION93.6
3.73-27.780.14481700.12733215X-RAY DIFFRACTION91.88
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5832637926370.163951332885-0.05006392757830.520721857173-0.07421131994870.445132687729-0.00166323765680.00479992630680.0480051615773-0.01529298734380.0125622616899-0.0303689071838-0.0202025811760.01689315667952.99220153231E-50.09303745178260.01167273129541.74887347717E-50.09002815944890.002067276617070.09294027926295.382359330954.32364216751-2.83868728359
20.232676965880.0089625046926-0.04757498570850.3275143506750.003241503433270.305499867577-0.0409306947079-0.1015821982750.1352196339140.0655011014824-0.009693322285190.049969763389-0.06762429365570.02063110146471.70870359154E-50.17328321160.00862584411159-0.01021987129660.156072729525-0.0201209072590.161403321782-2.711073711697.404555112316.0098525502
30.633883271640.154541403221-0.121240392760.442870996432-0.06778131281280.3212833843310.002732795349860.0181851382587-0.0360625606466-0.00412989152557-0.001025297894420.01566293422240.01890797106830.0260212490964-1.75088478357E-50.1300541715950.006202121411570.0009213176883270.116762015152-0.003877270735680.128661492064-1.99742049166-4.45534888505-3.27597772695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 128 )9 - 1281 - 120
22chain 'A' and (resid 129 through 218 )129 - 218121 - 210
33chain 'A' and (resid 219 through 393 )219 - 393211 - 385

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