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- PDB-9vsm: Crystal structure of cystathionine gamma-synthase from Lactobacil... -

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Basic information

Entry
Database: PDB / ID: 9vsm
TitleCrystal structure of cystathionine gamma-synthase from Lactobacillus plantarum complexed with the cystathionine-bound external aldimine
ComponentsCysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
KeywordsTRANSFERASE / cystathionine gamma-synthase
Function / homology
Function and homology information


carbon-sulfur lyase activity / cystathionine gamma-synthase / cystathionine gamma-synthase 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
Chem-E9U / Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Lett. / Year: 2026
Title: Structural insight into the substrate specificity of cystathionine gamma-synthase from Lactobacillus plantarum.
Authors: Matoba, Y. / Oda, K. / Ohtani, M. / Mende, Y. / Noda, K.
History
DepositionJul 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
B: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
C: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
D: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,0728
Polymers166,2674
Non-polymers1,8064
Water27,0231500
1
A: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
B: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
hetero molecules

A: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
B: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,0728
Polymers166,2674
Non-polymers1,8064
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area21940 Å2
ΔGint-89 kcal/mol
Surface area43670 Å2
MethodPISA
2
C: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
D: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
hetero molecules

C: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
D: Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,0728
Polymers166,2674
Non-polymers1,8064
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area22010 Å2
ΔGint-89 kcal/mol
Surface area43850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.987, 110.656, 107.388
Angle α, β, γ (deg.)90.00, 111.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-525-

HOH

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Components

#1: Protein
Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase


Mass: 41566.707 Da / Num. of mol.: 4 / Mutation: K203A
Source method: isolated from a genetically manipulated source
Details: This protein was C-terminally fused with histidine tag.
Source: (gene. exp.) Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1) (bacteria)
Gene: cgs, lp_2634 / Plasmid: plasmid / Details (production host): pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: F9URD2, cystathionine gamma-synthase
#2: Chemical
ChemComp-E9U / (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid


Mass: 451.389 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N3O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.58→48.36 Å / Num. obs: 230342 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Χ2: 1.14 / Net I/σ(I): 13 / Num. measured all: 1630623
Reflection shellResolution: 1.58→1.61 Å / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.455 / Num. measured all: 82272 / Num. unique obs: 11380 / CC1/2: 0.941 / Rpim(I) all: 0.182 / Rrim(I) all: 0.491 / Χ2: 0.91 / Net I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→46.79 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1707 11564 5.02 %
Rwork0.1508 --
obs0.1518 230325 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11299 0 116 1500 12915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611856
X-RAY DIFFRACTIONf_angle_d0.86816223
X-RAY DIFFRACTIONf_dihedral_angle_d8.0581703
X-RAY DIFFRACTIONf_chiral_restr0.0561936
X-RAY DIFFRACTIONf_plane_restr0.0062098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.22093830.17737263X-RAY DIFFRACTION100
1.6-1.620.19284050.16937242X-RAY DIFFRACTION100
1.62-1.640.20823890.16917209X-RAY DIFFRACTION100
1.64-1.660.19293990.16617305X-RAY DIFFRACTION100
1.66-1.680.20353770.15837344X-RAY DIFFRACTION100
1.68-1.70.18123660.16147267X-RAY DIFFRACTION100
1.7-1.730.17663680.15577215X-RAY DIFFRACTION100
1.73-1.750.19463820.16037270X-RAY DIFFRACTION100
1.75-1.780.19413800.16137270X-RAY DIFFRACTION100
1.78-1.810.19373780.15837301X-RAY DIFFRACTION100
1.81-1.840.18223910.15627273X-RAY DIFFRACTION100
1.84-1.870.20983950.16117268X-RAY DIFFRACTION100
1.87-1.910.18824240.15967246X-RAY DIFFRACTION100
1.91-1.950.18153940.15617250X-RAY DIFFRACTION100
1.95-1.990.19513400.15467321X-RAY DIFFRACTION100
1.99-2.040.17963770.15277243X-RAY DIFFRACTION100
2.04-2.090.17334200.14937220X-RAY DIFFRACTION100
2.09-2.140.17943830.15347283X-RAY DIFFRACTION100
2.14-2.210.17713580.15277300X-RAY DIFFRACTION100
2.21-2.280.16733820.14747332X-RAY DIFFRACTION100
2.28-2.360.17773830.14997281X-RAY DIFFRACTION100
2.36-2.450.17123690.15787354X-RAY DIFFRACTION100
2.45-2.570.17083980.15377256X-RAY DIFFRACTION100
2.57-2.70.1683630.15157347X-RAY DIFFRACTION100
2.7-2.870.17143830.15587319X-RAY DIFFRACTION100
2.87-3.090.16543880.15467335X-RAY DIFFRACTION100
3.09-3.40.16373930.1497305X-RAY DIFFRACTION100
3.4-3.90.16294170.14217316X-RAY DIFFRACTION100
3.9-4.910.13893920.1287361X-RAY DIFFRACTION100
4.91-46.790.16383870.1557465X-RAY DIFFRACTION100

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