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- PDB-9d2d: E. coli cysteine desulfurase SufS R359A -

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Basic information

Entry
Database: PDB / ID: 9d2d
TitleE. coli cysteine desulfurase SufS R359A
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / iron-sulfur / cysteine / PLP / desulfurase / Fe-S
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 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 desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsDunkle, J.A. / Frantom, P.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142966 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112919 United States
National Science Foundation (NSF, United States)CHE1828078 United States
CitationJournal: Biochemistry / Year: 2025
Title: A Role for Two Conserved Arginine Residues in Protected Persulfide Transfer by SufE-Dependent SufS Cysteine Desulfurases.
Authors: Gogar, R.K. / Conte, J.V. / Chhikara, N. / Dunkle, J.A. / Frantom, P.A.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6582
Polymers44,6231
Non-polymers351
Water52229
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3164
Polymers89,2452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8040 Å2
ΔGint-63 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.140, 126.140, 133.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

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Components

#1: Protein Cysteine desulfurase / Cysteine sulfinate desulfinase / CSD / Selenocysteine beta-lyase / SCL / Selenocysteine lyase / ...Cysteine sulfinate desulfinase / CSD / Selenocysteine beta-lyase / SCL / Selenocysteine lyase / Selenocysteine reductase


Mass: 44622.594 Da / Num. of mol.: 1 / Mutation: R359A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufS, csdB, ynhB, b1680, JW1670 / Production host: Escherichia coli (E. coli) / References: UniProt: P77444, cysteine desulfurase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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: 5.98 Å3/Da / Density % sol: 79.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 4-4.5 M NaCl, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→45.83 Å / Num. obs: 27454 / % possible obs: 90.9 % / Redundancy: 10.59 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 19.31
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.801

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→42.3 Å / SU ML: 0.345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.382
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.245 2007 7.32 %
Rwork0.21 --
obs0.213 27426 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 1 29 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083199
X-RAY DIFFRACTIONf_angle_d0.9544358
X-RAY DIFFRACTIONf_dihedral_angle_d8.013441
X-RAY DIFFRACTIONf_chiral_restr0.053491
X-RAY DIFFRACTIONf_plane_restr0.011566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.37061610.34121899X-RAY DIFFRACTION97
2.77-2.840.32651460.25721971X-RAY DIFFRACTION100
2.84-2.930.31071500.21941962X-RAY DIFFRACTION100
2.93-3.020.24861630.22271963X-RAY DIFFRACTION100
3.02-3.130.2741550.21871957X-RAY DIFFRACTION100
3.13-3.250.2381570.24671964X-RAY DIFFRACTION100
3.25-3.40.29621440.26671907X-RAY DIFFRACTION95
3.4-3.580.281800.2531079X-RAY DIFFRACTION55
3.58-3.80.3331030.25791147X-RAY DIFFRACTION58
3.81-4.10.28941140.25871351X-RAY DIFFRACTION68
4.1-4.510.18131570.16261996X-RAY DIFFRACTION100
4.51-5.160.18961560.16382020X-RAY DIFFRACTION100
5.16-6.50.22371620.18162057X-RAY DIFFRACTION100
6.5-42.30.1841590.16242146X-RAY DIFFRACTION98

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