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- PDB-8biz: Cystathionine gamma-lyase from Toxoplasma gondii in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8biz
TitleCystathionine gamma-lyase from Toxoplasma gondii in complex with cysteine
ComponentsCystathionine beta-lyase, putative
KeywordsCYTOSOLIC PROTEIN / Transsulfuration pathway / hydrogen sulfide / cysteine / toxoplasma
Function / homology
Function and homology information


plant cystathionine gamma-synthase / carbon-sulfur lyase 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
CYSTEINE / PYRIDOXAL-5'-PHOSPHATE / plant cystathionine gamma-synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 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 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)92,6466
Polymers91,9092
Non-polymers7374
Water9,368520
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)185,29112
Polymers183,8184
Non-polymers1,4738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area25510 Å2
ΔGint-162 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.346, 158.346, 94.213
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-746-

HOH

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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-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-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 12% (w/v) PEG 3350, 0.1M sodium citrate pH 4.6, CYMAL-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→45.412 Å / Num. obs: 108481 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 28.4
Reflection shellResolution: 1.89→1.92 Å / Num. unique obs: 5370 / CC1/2: 0.892

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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: 1.891→45.412 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 5530 5.1 %
Rwork0.1705 --
obs0.1713 108472 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.891→45.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6017 0 44 520 6581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066250
X-RAY DIFFRACTIONf_angle_d0.9198494
X-RAY DIFFRACTIONf_dihedral_angle_d6.4475114
X-RAY DIFFRACTIONf_chiral_restr0.058939
X-RAY DIFFRACTIONf_plane_restr0.0061091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.891-1.91240.23072290.20733351X-RAY DIFFRACTION100
1.9124-1.93490.22781650.19263431X-RAY DIFFRACTION100
1.9349-1.95850.19122170.18583384X-RAY DIFFRACTION100
1.9585-1.98330.19172090.18673369X-RAY DIFFRACTION100
1.9833-2.00940.21331690.18913385X-RAY DIFFRACTION100
2.0094-2.03690.19991680.18453415X-RAY DIFFRACTION100
2.0369-2.0660.22461960.18933405X-RAY DIFFRACTION100
2.066-2.09680.18181880.18833428X-RAY DIFFRACTION100
2.0968-2.12960.20971880.18223353X-RAY DIFFRACTION100
2.1296-2.16450.21191650.18413476X-RAY DIFFRACTION100
2.1645-2.20180.18341740.18093404X-RAY DIFFRACTION100
2.2018-2.24190.20621750.17873413X-RAY DIFFRACTION100
2.2419-2.2850.18761660.17493444X-RAY DIFFRACTION100
2.285-2.33160.21351840.18123424X-RAY DIFFRACTION100
2.3316-2.38230.20121780.17743387X-RAY DIFFRACTION100
2.3823-2.43770.20211670.18573453X-RAY DIFFRACTION100
2.4377-2.49870.19911770.18213405X-RAY DIFFRACTION100
2.4987-2.56630.18581990.17873419X-RAY DIFFRACTION100
2.5663-2.64180.19742010.18413418X-RAY DIFFRACTION100
2.6418-2.7270.21611810.18453420X-RAY DIFFRACTION100
2.727-2.82450.18591880.18033445X-RAY DIFFRACTION100
2.8245-2.93750.18842020.17113429X-RAY DIFFRACTION100
2.9375-3.07120.19251810.17893410X-RAY DIFFRACTION100
3.0712-3.23310.18991690.17133489X-RAY DIFFRACTION100
3.2331-3.43560.1842050.16423408X-RAY DIFFRACTION100
3.4356-3.70070.15121640.15163470X-RAY DIFFRACTION100
3.7007-4.07290.17351640.15493487X-RAY DIFFRACTION100
4.0729-4.66180.15771960.14473471X-RAY DIFFRACTION100
4.6618-5.87140.1841550.16273538X-RAY DIFFRACTION100
5.8714-45.4120.17062100.16413611X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -75.084 Å / Origin y: -1.2631 Å / Origin z: 29.1133 Å
111213212223313233
T0.112 Å20.0074 Å20.0047 Å2-0.0809 Å20.0048 Å2--0.082 Å2
L0.0641 °20.0874 °20.0246 °2-0.6523 °20.0312 °2--0.1632 °2
S0.0099 Å °0.021 Å °-0.013 Å °-0.1207 Å °0.0024 Å °0.0043 Å °-0.0119 Å °0.0081 Å °0 Å °
Refinement TLS groupSelection details: all

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