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- PDB-8vbs: E. coli cysteine desulfurase SufS bound to SufE C51A -

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Basic information

Entry
Database: PDB / ID: 8vbs
TitleE. coli cysteine desulfurase SufS bound to SufE C51A
Components
  • Cysteine desulfurase
  • Cysteine desulfuration protein SufE
KeywordsTRANSFERASE / pyridoxal 5'-phosphate / cysteine desulfurase / transpersulfurase / iron-sulfur cluster / persulfide
Function / homology
Function and homology information


selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly ...selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / sulfur compound metabolic process / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Cysteine desulfuration protein SufE / Fe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / Cysteine desulfurase, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Cysteine desulfuration protein SufE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsDunkle, J.A. / Frantom, P.A. / Gilbert, N.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142966 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112919 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structure of the SufS-SufE complex reveals interactions driving protected persulfide transfer in iron-sulfur cluster biogenesis.
Authors: Gogar, R.K. / Chhikara, N. / Vo, M. / Gilbert, N.C. / Dunkle, J.A. / Frantom, P.A.
History
DepositionDec 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
C: Cysteine desulfuration protein SufE
B: Cysteine desulfurase
D: Cysteine desulfuration protein SufE


Theoretical massNumber of molelcules
Total (without water)121,0004
Polymers121,0004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.492, 130.567, 101.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Cysteine desulfurase


Mass: 44740.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufS / Production host: Escherichia coli (E. coli) / References: UniProt: P77444, cysteine desulfurase
#2: Protein Cysteine desulfuration protein SufE


Mass: 15759.246 Da / Num. of mol.: 2 / Mutation: C51A, E107C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufE / Production host: Escherichia coli (E. coli) / References: UniProt: J7Q7S7
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 24.5-31.5% w/v PEG2000 MME, 0.1 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.31→79.97 Å / Num. obs: 15872 / % possible obs: 85.1 % / Redundancy: 11.23 % / Biso Wilson estimate: 95.61 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.87
Reflection shellResolution: 3.31→3.51 Å / Redundancy: 12.08 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 4.28 / % possible all: 53.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→60.22 Å / SU ML: 0.437 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.292
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.272 2948 10.03 %
Rwork0.231 --
obs0.235 15754 84.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 148 Å2
Refinement stepCycle: LAST / Resolution: 3.31→60.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8374 0 0 0 8374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038550
X-RAY DIFFRACTIONf_angle_d0.51411618
X-RAY DIFFRACTIONf_dihedral_angle_d10.5463104
X-RAY DIFFRACTIONf_chiral_restr0.0541307
X-RAY DIFFRACTIONf_plane_restr0.0051505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.370.4649780.3679718X-RAY DIFFRACTION48
3.37-3.420.3034840.3374777X-RAY DIFFRACTION52
3.42-3.490.4229940.2943865X-RAY DIFFRACTION57
3.49-3.550.3781970.2946894X-RAY DIFFRACTION61
3.55-3.630.36821090.2909992X-RAY DIFFRACTION65
3.63-3.70.31931220.29961035X-RAY DIFFRACTION71
3.7-3.790.35031250.29311123X-RAY DIFFRACTION74
3.79-3.890.37381300.29291188X-RAY DIFFRACTION80
3.89-3.990.33391400.27621252X-RAY DIFFRACTION84
3.99-4.110.31391540.27131355X-RAY DIFFRACTION90
4.11-4.240.27821630.27131445X-RAY DIFFRACTION98
4.24-4.390.26441640.27051503X-RAY DIFFRACTION99
4.39-4.570.25371700.23381451X-RAY DIFFRACTION99
4.57-4.780.29851610.23631468X-RAY DIFFRACTION99
4.78-5.030.28621610.24551492X-RAY DIFFRACTION99
5.03-5.340.33431640.23511471X-RAY DIFFRACTION99
5.34-5.750.29031620.24871471X-RAY DIFFRACTION99
5.75-6.330.2781710.261502X-RAY DIFFRACTION100
6.33-7.250.2611630.23921472X-RAY DIFFRACTION98
7.25-9.130.1951700.16781483X-RAY DIFFRACTION100
9.13-60.220.1991660.14811484X-RAY DIFFRACTION99
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)
11.5620.2788-0.16943.18910.70916.0137-0.2834-0.20150.4946-0.3146-0.07880.1524-2.6325-0.18340.32272.76190.453-0.39590.9843-0.09320.8462.36726.65821.849
27.8573-1.607-1.46814.7541-0.68890.5546-0.44250.3816-0.5426-0.13430.1320.0213-1.12920.17380.2922.01460.2969-0.13261.5753-0.08460.748820.76812.90151.722
32.68870.1357-0.25191.54380.24464.9026-0.4077-0.07950.33840.0415-0.0994-0.3669-1.45610.74530.51541.8873-0.1746-0.17670.94840.23680.810525.87711.3727.53
45.6861-1.0452-0.25562.99321.04150.40940.62650.69560.31930.3586-0.39670.294-1.8346-0.2028-0.25752.67440.48780.10751.8280.17230.83067.59223.491-24.944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2:405 )
2X-RAY DIFFRACTION2CHAIN C AND RESID 3:138 )
3X-RAY DIFFRACTION3CHAIN B AND RESID 2:405 )
4X-RAY DIFFRACTION4CHAIN D AND RESID 3:137 )

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