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- PDB-8biw: Cystathionine gamma-lyase N360S mutant in complex with DL-proparg... -

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Basic information

Entry
Database: PDB / ID: 8biw
TitleCystathionine gamma-lyase N360S mutant in complex with DL-propargylglycine
ComponentsCystathionine beta-lyase, putative
KeywordsCYTOSOLIC PROTEIN / transsulfuration pathway / hydrogen sulfide / propargylglycine / toxoplasma
Function / homology
Function and homology information


cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
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
(2S)-2-aminopent-4-enoic acid / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase, putative
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsFernandez-Rodriguez, C. / Conter, C. / Oyenarte, I. / Favretto, F. / Quintana, I. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.A.
Funding support Spain, Italy, 3items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2010-17857 and Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2019-109055RB-I00 Spain
Ministero dell Universita e della Ricerca2017ZBBYNC Italy
CitationJournal: Protein Sci. / Year: 2023
Title: Structural basis of the inhibition of cystathionine gamma-lyase from Toxoplasma gondii by propargylglycine and cysteine.
Authors: Fernandez-Rodriguez, C. / Conter, C. / Oyenarte, I. / Favretto, F. / Quintana, I. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.A.
History
DepositionNov 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Cystathionine beta-lyase, putative
A: Cystathionine beta-lyase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6346
Polymers91,9092
Non-polymers7254
Water4,972276
1
E: Cystathionine beta-lyase, putative
A: Cystathionine beta-lyase, putative
hetero molecules

E: Cystathionine beta-lyase, putative
A: Cystathionine beta-lyase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,26712
Polymers183,8184
Non-polymers1,4498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area25670 Å2
ΔGint-151 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.028, 158.028, 93.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Cystathionine beta-lyase, putative / / Putative cystathione gamma lyase


Mass: 45954.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: BN1205_096960, TGVEG_312930 / Production host: Escherichia coli (E. coli) / References: UniProt: B6K8Y1, cystathionine gamma-lyase
#2: Chemical ChemComp-2AG / (2S)-2-aminopent-4-enoic acid / L-allylglycine / Allylglycine


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 12% (w/v) PEG 3350 0.1M sodium citrate pH 4.6, CYMAL-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.98→77.26 Å / Num. obs: 92916 / % possible obs: 99.4 % / Redundancy: 17.4 % / CC1/2: 0.999 / Net I/σ(I): 21.9
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 4268 / CC1/2: 0.544

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Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHENIX1.18refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMP

2nmp


Resolution: 1.981→77.259 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 4597 4.95 %
Rwork0.175 --
obs0.1762 92909 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.981→77.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 16 276 6282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176170
X-RAY DIFFRACTIONf_angle_d1.4858372
X-RAY DIFFRACTIONf_dihedral_angle_d6.0925022
X-RAY DIFFRACTIONf_chiral_restr0.096946
X-RAY DIFFRACTIONf_plane_restr0.011076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9813-2.00380.29381350.25662681X-RAY DIFFRACTION91
2.0038-2.02740.28691330.26142799X-RAY DIFFRACTION95
2.0274-2.05210.30371410.24452867X-RAY DIFFRACTION98
2.0521-2.07810.2541720.22732916X-RAY DIFFRACTION99
2.0781-2.10540.24311560.2152898X-RAY DIFFRACTION100
2.1054-2.13430.23771660.20642946X-RAY DIFFRACTION100
2.1343-2.16480.24921700.20562900X-RAY DIFFRACTION100
2.1648-2.19710.25991240.19232956X-RAY DIFFRACTION100
2.1971-2.23140.22071450.19092967X-RAY DIFFRACTION100
2.2314-2.2680.23381720.1892942X-RAY DIFFRACTION100
2.268-2.30710.23191650.18592889X-RAY DIFFRACTION100
2.3071-2.34910.21961460.19142986X-RAY DIFFRACTION100
2.3491-2.39430.21561780.18262905X-RAY DIFFRACTION100
2.3943-2.44310.1951350.17792964X-RAY DIFFRACTION100
2.4431-2.49630.22241440.17872960X-RAY DIFFRACTION100
2.4963-2.55430.20851800.1742925X-RAY DIFFRACTION100
2.5543-2.61820.1881390.18112937X-RAY DIFFRACTION100
2.6182-2.6890.21571620.18282939X-RAY DIFFRACTION100
2.689-2.76810.19131720.17432956X-RAY DIFFRACTION100
2.7681-2.85750.21321580.17522953X-RAY DIFFRACTION100
2.8575-2.95960.21811460.17662964X-RAY DIFFRACTION100
2.9596-3.07810.23071560.17982949X-RAY DIFFRACTION100
3.0781-3.21820.19241590.1772989X-RAY DIFFRACTION100
3.2182-3.38790.1851360.17022945X-RAY DIFFRACTION100
3.3879-3.60020.18521550.16293026X-RAY DIFFRACTION100
3.6002-3.87810.18311630.16212947X-RAY DIFFRACTION100
3.8781-4.26840.16621450.15583017X-RAY DIFFRACTION100
4.2684-4.88590.15371590.14362989X-RAY DIFFRACTION100
4.8859-6.15540.19521330.17013051X-RAY DIFFRACTION100
6.1554-77.2550.17071520.1643149X-RAY DIFFRACTION100

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