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- PDB-8srt: Crystal structure of the O-acetyl-L-serine sulfhydrylase A (CysK)... -

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Basic information

Entry
Database: PDB / ID: 8srt
TitleCrystal structure of the O-acetyl-L-serine sulfhydrylase A (CysK) holoenzyme from Staphylococcus aureus NCTC 8325
ComponentsCysteine synthase
KeywordsTRANSFERASE / Pyridoxal-phosphate dependent enzyme
Function / homology
Function and homology information


L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPederick, J.L. / Vandborg, B.C. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Identification of Cysteine Metabolism Regulator (CymR)-Derived Pentapeptides as Nanomolar Inhibitors of Staphylococcus aureus O -Acetyl-l-serine Sulfhydrylase (CysK).
Authors: Pederick, J.L. / Vandborg, B.C. / George, A. / Bovermann, H. / Boyd, J.M. / Freundlich, J.S. / Bruning, J.B.
History
DepositionMay 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)68,5162
Polymers68,5162
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-21 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.985, 96.038, 58.597
Angle α, β, γ (deg.)90.000, 112.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cysteine synthase


Mass: 34257.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: SAOUHSC_00488 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G0Q8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→35.95 Å / Num. obs: 44294 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 13 / Num. measured all: 301349 / Scaling rejects: 54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.946.71.0151907428370.7160.4211.11.899.8
9.11-35.956.60.02727474150.9990.0110.02941.297.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q3B

2q3b


Resolution: 1.9→35.95 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 2214 5 %
Rwork0.1873 42045 -
obs0.189 44259 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94 Å2 / Biso mean: 43.7348 Å2 / Biso min: 25.58 Å2
Refinement stepCycle: final / Resolution: 1.9→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4489 0 0 233 4722
Biso mean---46.57 -
Num. residues----618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.940.32471490.268825932742100
1.94-1.990.28651500.247226112761100
1.99-2.040.30751590.24326102769100
2.04-2.090.2841520.222626062758100
2.09-2.150.27411010.215226132714100
2.15-2.220.26761190.20926512770100
2.22-2.30.27571360.203626572793100
2.3-2.390.28871330.216526182751100
2.39-2.50.27791230.207426542777100
2.5-2.630.2511540.216926052759100
2.63-2.80.25861630.212426042767100
2.8-3.020.27461380.214826182756100
3.02-3.320.2721260.20826472773100
3.32-3.80.20531310.17226442775100
3.8-4.780.16241240.150226562780100
4.78-35.950.16681560.16482658281499

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