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- PDB-8amp: Crystal structure of M.tuberculosis ferredoxin Fdx -

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Basic information

Entry
Database: PDB / ID: 8amp
TitleCrystal structure of M.tuberculosis ferredoxin Fdx
ComponentsPossible ferredoxin
KeywordsELECTRON TRANSPORT / Ferredoxin / tuberculosis / Rv0763c / CYP51
Function / homology4Fe-4S single cluster domain / : / 3 iron, 4 sulfur cluster binding / metal ion binding / FE3-S4 CLUSTER / : / Ferredoxin Fdx
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBukhdruker, S. / Kavaleuski, A. / Marin, E. / Kapranov, I. / Mishin, A. / 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: Possible ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8713
Polymers8,5201
Non-polymers3522
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-27 kcal/mol
Surface area3750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.959, 46.959, 162.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-102-

FE

21A-201-

HOH

31A-205-

HOH

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Components

#1: Protein Possible ferredoxin


Mass: 8519.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0763c / Production host: Escherichia coli (E. coli) / References: UniProt: P71820
#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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2→28.76 Å / Num. obs: 4958 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 38.46 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.097 / Net I/σ(I): 10.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.059.90.933460.5262.801100
2.05-2.119.81.323610.6871.99799.4
2.11-2.179.51.623380.7941.621100
2.17-2.249.12.073390.8141.252100
2.24-2.3192.63030.8740.97692
2.31-2.399.63.33190.9230.793100
2.39-2.4810.34.273030.9510.6499.7
2.48-2.589.95.382840.9740.463100
2.58-2.7106.322810.9820.393100
2.7-2.839.8102640.9920.222100
2.83-2.989.611.192490.9920.197100
2.98-3.169.213.12470.9960.14100
3.16-3.388.717.052340.9970.099100
3.38-3.659.623.142200.9990.071100
3.65-49.727.871890.9990.063100
4-4.479.632.871880.9990.056100
4.47-5.178.733.151680.9990.053100
5.17-6.337.931.521330.9990.056100
6.33-8.958.335.291190.9990.051100
8.95-28.767.436.57730.9940.05196.1

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Processing

Software
NameVersionClassification
XDS20170615data reduction
STARANISO3.344 27-Apr-2022data scaling
MoRDa1.4.09; 10.02.2022phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJW

1vjw


Resolution: 2→28.76 Å / SU ML: 0.2447 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.4958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.291 416 10.1 %
Rwork0.2503 3703 -
obs0.2543 4119 83.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.8 Å2
Refinement stepCycle: LAST / Resolution: 2→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 8 5 487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.122495
X-RAY DIFFRACTIONf_angle_d4.4138680
X-RAY DIFFRACTIONf_chiral_restr2.093873
X-RAY DIFFRACTIONf_plane_restr0.004791
X-RAY DIFFRACTIONf_dihedral_angle_d14.073171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.290.3601980.3185869X-RAY DIFFRACTION60.17
2.29-2.880.34541460.31491290X-RAY DIFFRACTION87.72
2.89-28.760.26511720.22451544X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.2235812771 Å / Origin y: -10.5283877981 Å / Origin z: -13.6477102063 Å
111213212223313233
T0.169361525199 Å2-0.0369906789722 Å2-0.215263474863 Å2-0.313415454142 Å20.0664168035822 Å2--0.663810000722 Å2
L2.12669271625 °2-2.00557385106 °20.17651409912 °2-5.28127722827 °20.169499384196 °2--0.807417697391 °2
S0.203074986829 Å °0.0371668676423 Å °0.459390927478 Å °0.622434118087 Å °-0.0829792519237 Å °-3.2436368637 Å °-0.539500956334 Å °0.484072393083 Å °0.260567329696 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 202)

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