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

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Basic information

Entry
Database: PDB / ID: 8sru
TitleCrystal structure of O-acetyl-L-serine sulfhydrylase A (CysK) from Staphylococcus aureus NCTC 8325 complexed with a serine acetyltransferase (CysE) derived peptide
Components
  • Cysteine synthase
  • Serine acetyltransferase (CysE) derived peptide
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: 1.5 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: Cysteine synthase
D: Cysteine synthase
H: Serine acetyltransferase (CysE) derived peptide
E: Serine acetyltransferase (CysE) derived peptide
F: Serine acetyltransferase (CysE) derived peptide
G: Serine acetyltransferase (CysE) derived peptide


Theoretical massNumber of molelcules
Total (without water)141,7488
Polymers141,7488
Non-polymers00
Water19,6901093
1
A: Cysteine synthase
E: Serine acetyltransferase (CysE) derived peptide


Theoretical massNumber of molelcules
Total (without water)35,4372
Polymers35,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-5 kcal/mol
Surface area12870 Å2
MethodPISA
2
B: Cysteine synthase
F: Serine acetyltransferase (CysE) derived peptide


Theoretical massNumber of molelcules
Total (without water)35,4372
Polymers35,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area13760 Å2
MethodPISA
3
C: Cysteine synthase
G: Serine acetyltransferase (CysE) derived peptide


Theoretical massNumber of molelcules
Total (without water)35,4372
Polymers35,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area13120 Å2
MethodPISA
4
D: Cysteine synthase
H: Serine acetyltransferase (CysE) derived peptide


Theoretical massNumber of molelcules
Total (without water)35,4372
Polymers35,4372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.660, 96.738, 94.287
Angle α, β, γ (deg.)90.000, 93.090, 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.: 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
Serine acetyltransferase (CysE) derived peptide


Mass: 1179.235 Da / Num. of mol.: 4 / 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.: 1093 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 01M 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: Aug 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→39.05 Å / Num. obs: 184526 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 12.4 / Num. measured all: 1256372 / Scaling rejects: 115
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
1.5-1.536.81.2246113590110.6020.5041.3261.598.9
8.22-39.056.50.035696710730.9990.0150.0382991.1

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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: 1.5→39.05 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 9657 5.24 %
Rwork0.1852 174779 -
obs0.187 184436 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.18 Å2 / Biso mean: 29.4781 Å2 / Biso min: 15.39 Å2
Refinement stepCycle: final / Resolution: 1.5→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9315 0 0 1093 10408
Biso mean---37.54 -
Num. residues----1252
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 (%)
1.5-1.520.30213530.27095689604298
1.52-1.530.30263440.269758116155100
1.53-1.550.28313630.257657326095100
1.55-1.570.28953270.245258686195100
1.57-1.590.27213520.237957766128100
1.59-1.620.26713530.227157986151100
1.62-1.640.25863390.224157906129100
1.64-1.660.26813440.217257936137100
1.66-1.690.26253090.205858226131100
1.69-1.720.26313090.203758316140100
1.72-1.750.25052800.205659076187100
1.75-1.780.2473160.204357766092100
1.78-1.810.24593070.198558426149100
1.81-1.850.23933400.195258336173100
1.85-1.890.24693250.195158046129100
1.89-1.930.2233050.190958256130100
1.93-1.980.2513020.188458256127100
1.98-2.040.25693310.196558186149100
2.04-2.10.23623200.194958496169100
2.1-2.160.24072910.191358706161100
2.16-2.240.23373450.187558216166100
2.24-2.330.23193110.187958106121100
2.33-2.440.22633360.19258186154100
2.44-2.560.24313170.185258446161100
2.56-2.730.2122990.191958826181100
2.73-2.940.22332800.194659316211100
2.94-3.230.2242980.194258616159100
3.23-3.70.2043330.171358126145100
3.7-4.660.16383540.153158666220100
4.66-39.050.19162740.16835875614998

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