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- PDB-9khn: Crystal structure of human cystathionine gamma-lyase in complex w... -

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Basic information

Entry
Database: PDB / ID: 9khn
TitleCrystal structure of human cystathionine gamma-lyase in complex with L-aminoethoxyvinylglycine
ComponentsCystathionine gamma-lyase
KeywordsLYASE / CSE / PLP / AVG
Function / homology
Function and homology information


protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / L-cystine L-cysteine-lyase (deaminating) / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / homocysteine desulfhydrase activity / homocysteine desulfhydrase / Cysteine formation from homocysteine / cystathionine gamma-lyase / Degradation of cysteine and homocysteine ...protein sulfhydration / selenocystathionine gamma-lyase activity / positive regulation of aortic smooth muscle cell differentiation / L-cystine L-cysteine-lyase (deaminating) / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / homocysteine desulfhydrase activity / homocysteine desulfhydrase / Cysteine formation from homocysteine / cystathionine gamma-lyase / Degradation of cysteine and homocysteine / cystathionine gamma-lyase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / L-cysteine desulfhydrase activity / cysteine biosynthetic process via cystathionine / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / cysteine metabolic process / transsulfuration / negative regulation of apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to leukemia inhibitory factor / lipid metabolic process / pyridoxal phosphate binding / protein homotetramerization / calmodulin binding / positive regulation of canonical NF-kappaB signal transduction / extracellular exosome / identical protein binding / cytoplasm / cytosol
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-PPG / Cystathionine gamma-lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKukimoto-Niino, M. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human cystathionine gamma-lyase in complex with L-aminoethoxyvinylglycine
Authors: Kukimoto-Niino, M. / Shirouzu, M. / Honda, K.
History
DepositionNov 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,9008
Polymers177,3434
Non-polymers1,5574
Water18,4651025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22070 Å2
ΔGint-151 kcal/mol
Surface area43830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.214, 151.711, 83.524
Angle α, β, γ (deg.)90.00, 110.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cystathionine gamma-lyase / CGL / CSE / Cysteine desulfhydrase / Cysteine-protein sulfhydrase / Gamma-cystathionase / ...CGL / CSE / Cysteine desulfhydrase / Cysteine-protein sulfhydrase / Gamma-cystathionase / Homocysteine desulfhydrase


Mass: 44335.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTH / Production host: Escherichia coli (E. coli)
References: UniProt: P32929, cystathionine gamma-lyase, homocysteine desulfhydrase
#2: Chemical
ChemComp-PPG / (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid


Mass: 389.298 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1025 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MPD, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 95999 / % possible obs: 97.6 % / Redundancy: 3.1 % / Rsym value: 0.206 / Net I/σ(I): 5.3
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9680 / Rsym value: 0.86 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp


Resolution: 2→46.592 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.48
RfactorNum. reflection% reflection
Rfree0.2155 4811 5.01 %
Rwork0.17 --
obs0.1723 95943 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12086 0 104 1025 13215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812468
X-RAY DIFFRACTIONf_angle_d1.08816920
X-RAY DIFFRACTIONf_dihedral_angle_d15.064532
X-RAY DIFFRACTIONf_chiral_restr0.0421914
X-RAY DIFFRACTIONf_plane_restr0.0052176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.01810.31221000.26351936X-RAY DIFFRACTION62
2.0181-2.04190.27971710.25783096X-RAY DIFFRACTION98
2.0419-2.06680.28611610.25123087X-RAY DIFFRACTION98
2.0668-2.09290.30251550.24363088X-RAY DIFFRACTION98
2.0929-2.12050.28871650.23573091X-RAY DIFFRACTION98
2.1205-2.14950.28631810.22493053X-RAY DIFFRACTION99
2.1495-2.18020.26031680.22653122X-RAY DIFFRACTION98
2.1802-2.21280.26771600.22323082X-RAY DIFFRACTION99
2.2128-2.24730.27391490.23213143X-RAY DIFFRACTION98
2.2473-2.28420.28941500.21623081X-RAY DIFFRACTION98
2.2842-2.32360.24481620.2033114X-RAY DIFFRACTION99
2.3236-2.36580.27681580.19773110X-RAY DIFFRACTION99
2.3658-2.41130.25321510.18813109X-RAY DIFFRACTION99
2.4113-2.46050.24491700.19243085X-RAY DIFFRACTION98
2.4605-2.5140.23891600.18773112X-RAY DIFFRACTION99
2.514-2.57250.25211640.18353096X-RAY DIFFRACTION99
2.5725-2.63680.23881720.1763086X-RAY DIFFRACTION98
2.6368-2.70810.23221850.16673072X-RAY DIFFRACTION99
2.7081-2.78780.22551780.16963087X-RAY DIFFRACTION98
2.7878-2.87780.21021630.16293104X-RAY DIFFRACTION98
2.8778-2.98060.19551470.15593101X-RAY DIFFRACTION98
2.9806-3.09990.21191630.15073075X-RAY DIFFRACTION98
3.0999-3.2410.20371680.14863048X-RAY DIFFRACTION97
3.241-3.41180.17841460.14253073X-RAY DIFFRACTION97
3.4118-3.62550.19391670.13883039X-RAY DIFFRACTION96
3.6255-3.90530.16071580.1373011X-RAY DIFFRACTION95
3.9053-4.2980.15861520.12733029X-RAY DIFFRACTION96
4.298-4.91940.14711870.12232993X-RAY DIFFRACTION95
4.9194-6.19560.1911370.1453030X-RAY DIFFRACTION95
6.1956-46.5920.16251630.14412979X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -23.8832 Å / Origin y: -12.8472 Å / Origin z: 104.2388 Å
111213212223313233
T0.0699 Å2-0.0149 Å2-0.0036 Å2-0.0859 Å2-0.0048 Å2--0.0986 Å2
L0.1643 °2-0.0265 °2-0.0276 °2-0.2259 °20.0002 °2--0.2754 °2
S0.0031 Å °0.0001 Å °-0.039 Å °-0.0057 Å °-0.0107 Å °0.0096 Å °-0.0087 Å °0.0029 Å °0.0054 Å °
Refinement TLS groupSelection details: all

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