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

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Basic information

Entry
Database: PDB / ID: 8srv
TitleCrystal structure of O-acetyl-L-serine sulfhydrylase A (CysK) from Staphylococcus aureus NCTC 8325 complexed with a transcriptional repressor (CymR) derived 10 amino acid peptide
Components
  • Cysteine synthase
  • Transcriptional repressor (CymR) derived 10 amino acid peptide
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 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
B: Cysteine synthase
C: Transcriptional repressor (CymR) derived 10 amino acid peptide
D: Transcriptional repressor (CymR) derived 10 amino acid peptide


Theoretical massNumber of molelcules
Total (without water)71,0464
Polymers71,0464
Non-polymers00
Water12,412689
1
A: Cysteine synthase
D: Transcriptional repressor (CymR) derived 10 amino acid peptide


Theoretical massNumber of molelcules
Total (without water)35,5232
Polymers35,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area13210 Å2
MethodPISA
2
B: Cysteine synthase
C: Transcriptional repressor (CymR) derived 10 amino acid peptide


Theoretical massNumber of molelcules
Total (without water)35,5232
Polymers35,5232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.395, 96.240, 58.994
Angle α, β, γ (deg.)90.000, 111.920, 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: Protein/peptide Transcriptional repressor (CymR) derived 10 amino acid peptide


Mass: 1265.389 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 41.16 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaCl, 0.1 M PIPES pH 7, 22% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.32→36.14 Å / Num. obs: 136416 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 13.2 / Num. measured all: 918848 / Scaling rejects: 60
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
1.32-1.345.61.1513790167750.540.5281.2731.499
7.23-36.146.40.03354368460.9990.0140.03639.197.3

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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: 8SRT

8srt


Resolution: 1.32→35.42 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 6982 5.12 %
Rwork0.1644 129365 -
obs0.1656 136347 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.31 Å2 / Biso mean: 24.9638 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 1.32→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4742 0 0 689 5431
Biso mean---35.36 -
Num. residues----633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.32-1.330.31142550.29184211446699
1.34-1.350.28892140.271443204534100
1.35-1.370.28641970.266343114508100
1.37-1.380.27542190.244443484567100
1.38-1.40.24762550.232242954550100
1.4-1.420.24822120.224942964508100
1.42-1.440.26942240.224343434567100
1.44-1.460.24922120.213843434555100
1.46-1.490.22642440.199442904534100
1.49-1.510.21642390.191342944533100
1.51-1.540.19452390.186643034542100
1.54-1.570.20912250.179143054530100
1.57-1.60.1992290.176543244553100
1.6-1.630.19492430.173342874530100
1.63-1.660.22282270.17343414568100
1.66-1.70.18382120.168443314543100
1.7-1.740.19622270.170343254552100
1.74-1.790.19352360.16942964532100
1.79-1.840.20422560.181142924548100
1.84-1.90.18412490.176743024551100
1.9-1.970.21052360.1742884524100
1.97-2.050.21252160.173243414557100
2.05-2.140.20512440.1743024546100
2.14-2.260.17812500.162743124562100
2.26-2.40.19072600.163842814541100
2.4-2.580.19222100.168843744584100
2.58-2.840.19192160.168643134529100
2.84-3.250.21012390.16664320455999
3.26-4.10.15892390.13784317455699
4.1-35.420.1472580.13674360461899

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