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- PDB-8t2c: Crystal structure of O-acetyl-L-serine sulfhydrylase A (CysK) fro... -

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Basic information

Entry
Database: PDB / ID: 8t2c
TitleCrystal structure of O-acetyl-L-serine sulfhydrylase A (CysK) from Staphylococcus aureus NCTC 8325 complexed with a CymR pentapeptide
Components
  • Cysteine synthase
  • TYR-MET-PHE-TYR-ILE
KeywordsPROTEIN BINDING / Cysk / cysteine synthesis / CymR
Function / homology
Function and homology information


cysteine synthase / L-cysteine desulfhydrase activity / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPederick, J.L. / Bruning, J.B. / Vandborg, 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
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
C: TYR-MET-PHE-TYR-ILE
D: TYR-MET-PHE-TYR-ILE


Theoretical massNumber of molelcules
Total (without water)66,9364
Polymers66,9364
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-37 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.608, 94.515, 56.078
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cysteine synthase


Mass: 32732.176 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, cysteine synthase
#2: Protein/peptide TYR-MET-PHE-TYR-ILE


Mass: 735.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.82 Å3/Da / Density % sol: 32.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1M HEPES pH 7.5, 23-25% PEG3350

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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 EIGER X 9M / Detector: PIXEL / Date: Jan 30, 2023 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→47.26 Å / Num. obs: 46258 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Χ2: 0.97 / Net I/σ(I): 9.8 / Num. measured all: 319273
Reflection shellResolution: 1.8→1.84 Å / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.724 / Num. measured all: 19493 / Num. unique obs: 2716 / CC1/2: 0.618 / Rpim(I) all: 0.683 / Rrim(I) all: 1.856 / Χ2: 0.88 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.07 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1997 4.32 %
Rwork0.2227 --
obs0.2237 46187 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4462 0 0 148 4610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034541
X-RAY DIFFRACTIONf_angle_d0.5746179
X-RAY DIFFRACTIONf_dihedral_angle_d12.6431627
X-RAY DIFFRACTIONf_chiral_restr0.044721
X-RAY DIFFRACTIONf_plane_restr0.005804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.52631410.51033127X-RAY DIFFRACTION100
1.85-1.890.47551420.42033161X-RAY DIFFRACTION100
1.89-1.950.39691430.36743154X-RAY DIFFRACTION100
1.95-2.010.40621430.33263165X-RAY DIFFRACTION100
2.01-2.090.31351390.31913083X-RAY DIFFRACTION100
2.09-2.170.30721420.29453164X-RAY DIFFRACTION100
2.17-2.270.32891430.26523150X-RAY DIFFRACTION100
2.27-2.390.2831430.2363160X-RAY DIFFRACTION100
2.39-2.540.25731430.22623158X-RAY DIFFRACTION100
2.54-2.730.27991420.22643146X-RAY DIFFRACTION100
2.73-3.010.2531440.22593168X-RAY DIFFRACTION100
3.01-3.440.22571430.20413170X-RAY DIFFRACTION100
3.44-4.340.18471430.17633168X-RAY DIFFRACTION99
4.37-43.070.18281460.1733216X-RAY DIFFRACTION100

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