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

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Basic information

Entry
Database: PDB / ID: 8srw
TitleCrystal structure of O-acetyl-L-serine sulfhydrylase A (CysK) from Staphylococcus aureus NCTC 8325 complexed with a modified peptide inhibitor
Components
  • Cysteine synthase
  • TYR-MET-NAL-TYR-ILE
KeywordsTRANSFERASE / Pyridoxal-phosphate dependent enzyme
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: 2.15 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase
D: Cysteine synthase
B: Cysteine synthase
C: Cysteine synthase
E: TYR-MET-NAL-TYR-ILE
F: TYR-MET-NAL-TYR-ILE
G: TYR-MET-NAL-TYR-ILE
H: TYR-MET-NAL-TYR-ILE


Theoretical massNumber of molelcules
Total (without water)140,1758
Polymers140,1758
Non-polymers00
Water10,088560
1
A: Cysteine synthase
D: Cysteine synthase
E: TYR-MET-NAL-TYR-ILE
F: TYR-MET-NAL-TYR-ILE


Theoretical massNumber of molelcules
Total (without water)70,0884
Polymers70,0884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-21 kcal/mol
Surface area22050 Å2
MethodPISA
2
B: Cysteine synthase
C: Cysteine synthase
G: TYR-MET-NAL-TYR-ILE
H: TYR-MET-NAL-TYR-ILE


Theoretical massNumber of molelcules
Total (without water)70,0884
Polymers70,0884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-19 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.927, 119.714, 84.657
Angle α, β, γ (deg.)90.00, 98.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cysteine synthase


Mass: 34257.852 Da / Num. of mol.: 4
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: Protein/peptide
TYR-MET-NAL-TYR-ILE


Mass: 785.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 22-25% PEG 3350. Drops contained: 1ul 25 mg/ml CysK, 1 ul well solution, 0.4 ul CysK seed stock (1/100 dilution)

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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: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→39.9 Å / Num. obs: 70305 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.086 / Rrim(I) all: 0.23 / Χ2: 1 / Net I/σ(I): 8.9 / Num. measured all: 494112
Reflection shellResolution: 2.15→2.2 Å / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.85 / Num. measured all: 32948 / Num. unique obs: 4569 / CC1/2: 0.425 / Rpim(I) all: 0.738 / Rrim(I) all: 1.994 / Χ2: 0.91 / Net I/σ(I) obs: 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
Starting model: 8SRT

8srt


Resolution: 2.15→39.5 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 3517 5.01 %
Rwork0.1935 --
obs0.1956 70237 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9349 0 0 560 9909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029506
X-RAY DIFFRACTIONf_angle_d0.51712863
X-RAY DIFFRACTIONf_dihedral_angle_d7.4511358
X-RAY DIFFRACTIONf_chiral_restr0.0421456
X-RAY DIFFRACTIONf_plane_restr0.0051667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.30051420.28012689X-RAY DIFFRACTION100
2.18-2.210.31821380.28212678X-RAY DIFFRACTION100
2.21-2.240.33431430.28482649X-RAY DIFFRACTION100
2.24-2.280.35031380.26062686X-RAY DIFFRACTION100
2.28-2.320.27731140.26152679X-RAY DIFFRACTION100
2.32-2.360.29221480.25472709X-RAY DIFFRACTION99
2.36-2.40.29051610.25262576X-RAY DIFFRACTION100
2.4-2.440.3091290.24012700X-RAY DIFFRACTION99
2.44-2.490.27241330.24442632X-RAY DIFFRACTION99
2.49-2.550.27191370.23442679X-RAY DIFFRACTION99
2.55-2.610.31831340.23042627X-RAY DIFFRACTION99
2.61-2.670.26341510.2322614X-RAY DIFFRACTION98
2.67-2.750.2841420.22722671X-RAY DIFFRACTION100
2.75-2.830.25171530.21072667X-RAY DIFFRACTION100
2.83-2.920.26131270.21432692X-RAY DIFFRACTION100
2.92-3.020.28591290.21122687X-RAY DIFFRACTION100
3.02-3.140.24391430.2082674X-RAY DIFFRACTION100
3.14-3.290.22681350.19662682X-RAY DIFFRACTION100
3.29-3.460.22091370.1892663X-RAY DIFFRACTION100
3.46-3.680.20391490.1682692X-RAY DIFFRACTION100
3.68-3.960.18931390.15792665X-RAY DIFFRACTION100
3.96-4.360.19741290.14842678X-RAY DIFFRACTION100
4.36-4.990.19011510.14242650X-RAY DIFFRACTION98
4.99-6.280.22951370.17542664X-RAY DIFFRACTION99
6.28-39.50.19091780.1582717X-RAY DIFFRACTION100

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