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- PDB-9xlu: Crystal structure of Staphylococcus aureus cystathionine gamma-ly... -

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Basic information

Entry
Database: PDB / ID: 9xlu
TitleCrystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G
ComponentsCystathionine gamma-synthase homolog
KeywordsLYASE / cystathionine gamma-lyase / PLP-dependent enzyme / transsulfuration / Staphylococcus aureus
Function / homology
Function and homology information


cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / : / transsulfuration / : / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
: / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Cystathionine gamma-synthase homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLee, U. / Ha, N.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: To Be Published
Title: Family-Specialized Transformer for L-cystathionine gamma-lyase Engineering and Its Structural Interpretation
Authors: Lee, U. / Park, M. / Song, B. / Ha, N.C.
History
DepositionNov 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine gamma-synthase homolog


Theoretical massNumber of molelcules
Total (without water)43,2951
Polymers43,2951
Non-polymers00
Water4,071226
1
A: Cystathionine gamma-synthase homolog

A: Cystathionine gamma-synthase homolog

A: Cystathionine gamma-synthase homolog

A: Cystathionine gamma-synthase homolog


Theoretical massNumber of molelcules
Total (without water)173,1794
Polymers173,1794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10130 Å2
ΔGint-55 kcal/mol
Surface area46830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.832, 80.467, 161.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-500-

HOH

31A-593-

HOH

41A-597-

HOH

51A-599-

HOH

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Components

#1: Protein Cystathionine gamma-synthase homolog


Mass: 43294.820 Da / Num. of mol.: 1 / Mutation: V129G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: yrhB, SAV0460 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JQ19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 1.5% tryptone, 0.05M HEPES sodium pH 7.0, 0.01M sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 20, 2025
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→40.27 Å / Num. obs: 25074 / % possible obs: 87.21 % / Redundancy: 1.01 % / Biso Wilson estimate: 23.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.031 / Rrim(I) all: 0.089 / Net I/σ(I): 17.5
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 1 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 858 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→40.27 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2603 -9.95 %
Rwork0.2071 --
obs0.2123 25074 74.17 %
Refinement stepCycle: LAST / Resolution: 2.33→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 226 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.5833519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.370.3466860.2543571X-RAY DIFFRACTION36
2.37-2.420.3051960.2452769X-RAY DIFFRACTION47
2.42-2.470.29221020.2189910X-RAY DIFFRACTION54
2.47-2.530.26031030.22521023X-RAY DIFFRACTION60
2.53-2.590.2651150.21111155X-RAY DIFFRACTION67
2.59-2.660.27031180.21541237X-RAY DIFFRACTION71
2.66-2.740.26121160.2151341X-RAY DIFFRACTION77
2.74-2.830.26142450.20381309X-RAY DIFFRACTION83
2.83-2.930.2541330.19891503X-RAY DIFFRACTION87
2.93-3.050.25291310.19531574X-RAY DIFFRACTION90
3.05-3.190.28991420.20791609X-RAY DIFFRACTION93
3.19-3.350.26712790.20851499X-RAY DIFFRACTION95
3.36-3.570.28421460.19821510X-RAY DIFFRACTION88
3.57-3.840.25761380.1941439X-RAY DIFFRACTION83
3.84-4.230.22021370.19691292X-RAY DIFFRACTION76
4.23-4.840.23821430.18351312X-RAY DIFFRACTION77
4.84-6.090.2851350.20531372X-RAY DIFFRACTION81

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