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- PDB-8amq: Crystal structure of the complex CYP143-FdxE from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8amq
TitleCrystal structure of the complex CYP143-FdxE from M. tuberculosis
ComponentsProbable ferredoxin,Putative cytochrome P450 143
KeywordsOXIDOREDUCTASE / M. tuberculosis / cytochrome P450 / redox partner / ferredoxin / Rv1786 / Rv1785c / fusion / chimera
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 3 iron, 4 sulfur cluster binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
4Fe-4S single cluster domain / : / Alpha-Beta Plaits - #20 / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily ...4Fe-4S single cluster domain / : / Alpha-Beta Plaits - #20 / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / NICKEL (II) ION / Ferredoxin FdxE / Cytochrome P450 143
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBukhdruker, S. / Varaksa, T. / Smolskaya, S. / Marin, E. / Kapranov, I. / Kovalev, K. / 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: Probable ferredoxin,Putative cytochrome P450 143
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9709
Polymers53,7061
Non-polymers1,2648
Water8,557475
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-84 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.200, 54.354, 69.037
Angle α, β, γ (deg.)67.710, 77.210, 61.630
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 Probable ferredoxin,Putative cytochrome P450 143


Mass: 53705.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv1786, cyp143, Rv1785c, MTV049.07c / Production host: Escherichia coli (E. coli)
References: UniProt: O53937, UniProt: P9WPL3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01 M Nickel(II) chloride hexahydrate, 0.1 M Tris, 20% (w/v) PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→27.15 Å / Num. obs: 78791 / % possible obs: 94.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.46 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.147 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.643.20.3354690.123.03189
1.64-1.693.50.4356100.2012.5693.5
1.69-1.743.40.5654770.2492.09894.4
1.74-1.793.50.7353480.3321.70694.4
1.79-1.853.61.0452260.5281.26794.2
1.85-1.913.51.3850280.6090.96395.2
1.91-1.983.41.8148670.760.7495.5
1.98-2.073.42.5345590.8380.52792.9
2.07-2.163.53.4845590.9120.38996.2
2.16-2.263.44.243490.9270.31696.3
2.26-2.393.65.4741570.9630.23796.5
2.39-2.533.66.5639250.9710.19496.4
2.53-2.73.67.5836630.9760.16796.3
2.7-2.923.48.8133970.9830.13595.6
2.92-3.23.611.1231540.9880.10896.2
3.2-3.583.513.2728350.990.08796.4
3.58-4.133.615.3225320.9930.07396.8
4.13-5.063.415.9320860.9930.06994.7
5.06-7.163.415.5616350.9910.07596.3
7.16-27.153.417.379150.9890.0897.2

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AMP

8amp


Resolution: 1.6→27.15 Å / SU ML: 0.201 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.9816
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 3299 4.99 %
Rwork0.1766 62817 -
obs0.1782 66116 79.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.95 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 56 475 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0464116
X-RAY DIFFRACTIONf_angle_d1.85025673
X-RAY DIFFRACTIONf_chiral_restr0.7219611
X-RAY DIFFRACTIONf_plane_restr0.0103764
X-RAY DIFFRACTIONf_dihedral_angle_d14.28531558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.3648440.2975875X-RAY DIFFRACTION26.47
1.62-1.650.279570.29211147X-RAY DIFFRACTION34.73
1.65-1.670.3039840.28871430X-RAY DIFFRACTION44.13
1.67-1.70.2964830.28671602X-RAY DIFFRACTION48.84
1.7-1.730.3631790.2881814X-RAY DIFFRACTION54.65
1.73-1.760.2858880.29012008X-RAY DIFFRACTION61.02
1.76-1.80.30251290.29682199X-RAY DIFFRACTION66.97
1.8-1.830.32731330.28332465X-RAY DIFFRACTION75.07
1.83-1.870.28291370.27542603X-RAY DIFFRACTION79.05
1.87-1.910.27371550.2622797X-RAY DIFFRACTION85.39
1.92-1.960.31741600.25432933X-RAY DIFFRACTION89.55
1.96-2.020.28341400.23613106X-RAY DIFFRACTION94.09
2.02-2.080.27361620.21923011X-RAY DIFFRACTION92.7
2.08-2.140.25241650.20373194X-RAY DIFFRACTION96.36
2.14-2.220.24251740.19243164X-RAY DIFFRACTION96.09
2.22-2.310.22991640.17043174X-RAY DIFFRACTION96.64
2.31-2.410.18991660.16293173X-RAY DIFFRACTION96.36
2.41-2.540.20191800.16683133X-RAY DIFFRACTION96.59
2.54-2.70.19481670.16233165X-RAY DIFFRACTION96.55
2.7-2.910.20561650.16883163X-RAY DIFFRACTION95.69
2.91-3.20.20011740.16213148X-RAY DIFFRACTION96.35
3.2-3.660.18011730.15273178X-RAY DIFFRACTION96.63
3.66-4.610.13751560.12413166X-RAY DIFFRACTION96.68
4.61-27.150.14541640.13483169X-RAY DIFFRACTION96.22
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)
12.752562720620.9577480580870.4224172777431.689438284060.4487600727950.9760088316490.051398230737-0.0730601587324-0.1218708284860.08450744955050.00354379187246-0.05515158553290.08564212007240.0459829909723-0.0553129038280.1178273795230.01501941185970.005186457337510.0859803980490.01166252401310.12107554206983.308176281444.2275377884-1.26731843549
20.5557299614980.7245113915721.058848079221.205069141231.557348290834.96000862518-0.07911987577420.6002027920860.024271588969-0.5257042420870.127072814922-0.120596268301-0.1881220050920.515819297675-0.0376165812230.310575806006-0.01917206967270.02277955040720.3896363376860.005134102586830.14519785327582.855804803445.9203835131-28.8291859074
31.95919663961.101112904110.2830864539332.191307719140.214374253310.626115336307-0.010414681172-0.03653920165720.08911328677090.0107013355007-0.001442893573590.3305308015810.00828425974786-0.1105124684720.01226822215260.1165569684270.02198167594880.03067650673590.116214334636-0.01810397571670.14234223267571.896258204845.5685388799-2.94176755398
42.14065081794-0.337596152005-0.03380524254513.40052655931-0.4354714729561.639437483050.03699821632-0.2277903251210.2840544571920.3113209386690.08073938755180.696265117517-0.182347267411-0.16997649657-0.1298676379080.19307008617-0.008587800674480.07225783287420.161462301742-0.04554710864810.31989279798974.567794330762.96725225928.10143695592
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 1219 through 1393 )1219 - 1393290 - 464
22chain 'A' and (resid -5 through 74 )-5 - 741 - 80
33chain 'A' and (resid 1009 through 1128)1009 - 112881 - 199
44chain 'A' and (resid 1129 through 1218)1129 - 1218200 - 289

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