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- PDB-8bis: Crystal structure of cystathionine gamma-lyase from Toxoplasma go... -

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Basic information

Entry
Database: PDB / ID: 8bis
TitleCrystal structure of cystathionine gamma-lyase from Toxoplasma gondii in complex with DL-propargylglycine
ComponentsCystathionine beta-lyase, putative
KeywordsCYTOSOLIC PROTEIN / transsulfuration pathway / hydrogen sulfide / propargylglgycine / cystathionine gamma-lyase
Function / homology
Function and homology information


carbon-sulfur lyase activity / cystathionine gamma-synthase / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-2-aminopent-4-enoic acid / PYRIDOXAL-5'-PHOSPHATE / cystathionine gamma-synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.266 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, 6items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2010-17857 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2019-109055RB-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)BFU2013-47531-R Spain
Ministerio de Ciencia e Innovacion (MCIN)BFU2016-77408-R Spain
Ministero dell Universita e della RicercaFUR2020 Italy
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,5725
Polymers91,9632
Non-polymers6093
Water4,936274
1
C: Cystathionine beta-lyase, putative
A: Cystathionine beta-lyase, putative
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)185,14510
Polymers183,9264
Non-polymers1,2196
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area25210 Å2
ΔGint-156 kcal/mol
Surface area44820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.452, 157.452, 93.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-658-

HOH

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Components

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


Mass: 45981.520 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2AG / (2S)-2-aminopent-4-enoic acid / L-allylglycine


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 12% (w/v) PEG 3350, 0.1 M 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: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.26→45.452 Å / Num. obs: 61247 / % possible obs: 98.8 % / Redundancy: 26.8 % / CC1/2: 0.995 / Net I/σ(I): 14.2
Reflection shellResolution: 2.26→2.31 Å / Num. unique obs: 2656 / CC1/2: 0.641

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Processing

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

2nmp


Resolution: 2.266→45.452 Å / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.186 3047 4.98 %
Rwork0.162 --
obs0.1658 61235 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.266→45.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6047 0 8 274 6329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036241
X-RAY DIFFRACTIONf_angle_d0.688484
X-RAY DIFFRACTIONf_dihedral_angle_d5.5455060
X-RAY DIFFRACTIONf_chiral_restr0.044961
X-RAY DIFFRACTIONf_plane_restr0.0041095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2665-2.30550.34931480.28692492X-RAY DIFFRACTION81
2.3055-2.34750.22531260.20782743X-RAY DIFFRACTION89
2.3475-2.39260.22921640.20872821X-RAY DIFFRACTION92
2.3926-2.44140.24651660.20742904X-RAY DIFFRACTION95
2.4414-2.49450.24651390.21072882X-RAY DIFFRACTION95
2.4945-2.55250.24931630.21412928X-RAY DIFFRACTION95
2.5525-2.61640.20471550.19752920X-RAY DIFFRACTION95
2.6164-2.68710.21861420.20312932X-RAY DIFFRACTION95
2.6871-2.76620.22591630.19192928X-RAY DIFFRACTION95
2.7662-2.85540.23151580.1862910X-RAY DIFFRACTION95
2.8554-2.95750.18051570.17532915X-RAY DIFFRACTION95
2.9575-3.07580.20191850.18172891X-RAY DIFFRACTION94
3.0758-3.21580.19121020.17013030X-RAY DIFFRACTION97
3.2158-3.38530.19521580.16192920X-RAY DIFFRACTION95
3.3853-3.59730.18751260.15392976X-RAY DIFFRACTION96
3.5973-3.87490.18531720.14942914X-RAY DIFFRACTION94
3.8749-4.26450.1621520.13372988X-RAY DIFFRACTION95
4.2645-4.88090.13651500.11692973X-RAY DIFFRACTION95
4.8809-6.14680.1511640.14072985X-RAY DIFFRACTION95
6.1468-44.1040.15021520.14633120X-RAY DIFFRACTION95

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