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- PDB-8biu: Cystathionine gamma-lyase in complex with cystathionine -

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Basic information

Entry
Database: PDB / ID: 8biu
TitleCystathionine gamma-lyase in complex with cystathionine
ComponentsCystathionine beta-lyase, putative
KeywordsCYTOSOLIC PROTEIN / transsulfuration pathway / hydrogen sulfide / cystathionine / ketobutyrate
Function / homology
Function and homology information


plant cystathionine gamma-synthase / carbon-sulfur lyase activity / transsulfuration / methionine biosynthetic process / 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
2-KETOBUTYRIC ACID / PYRIDOXAL-5'-PHOSPHATE / plant cystathionine gamma-synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 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, 5items
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 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 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)92,5595
Polymers91,9632
Non-polymers5963
Water2,882160
1
G: Cystathionine beta-lyase, putative
A: Cystathionine beta-lyase, putative
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)185,11910
Polymers183,9264
Non-polymers1,1936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area25390 Å2
ΔGint-144 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.737, 157.737, 93.401
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: 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-2KT / 2-KETOBUTYRIC ACID / 2-OXOBUTANOIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.65 Å3/Da / Density % sol: 66.28 %
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: 0.9797 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: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.899→93.5 Å / Num. obs: 105469 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.992 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5190 / CC1/2: 0.461

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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: 1.899→93.401 Å / Cross valid method: NONE / σ(F): 18.88 / Phase error: 17.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1783 5201 4.93 %
Rwork0.1524 --
obs0.1632 105441 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→93.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 0 37 160 6174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066176
X-RAY DIFFRACTIONf_angle_d0.8628396
X-RAY DIFFRACTIONf_dihedral_angle_d7.3055014
X-RAY DIFFRACTIONf_chiral_restr0.05953
X-RAY DIFFRACTIONf_plane_restr0.0051083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.93130.25072600.22794922X-RAY DIFFRACTION95
1.9313-1.96640.22982610.20924969X-RAY DIFFRACTION95
1.9664-2.00420.222770.20844962X-RAY DIFFRACTION95
2.0042-2.04510.19962470.19264991X-RAY DIFFRACTION95
2.0451-2.08960.24322400.19185004X-RAY DIFFRACTION95
2.0896-2.13820.19332740.18774980X-RAY DIFFRACTION95
2.1382-2.19160.21762440.18844979X-RAY DIFFRACTION95
2.1916-2.25090.20932580.1764976X-RAY DIFFRACTION95
2.2509-2.31710.2142290.17865021X-RAY DIFFRACTION96
2.3171-2.39190.21762480.17644987X-RAY DIFFRACTION95
2.3919-2.47730.20222970.17884966X-RAY DIFFRACTION94
2.4773-2.57650.21442530.17525018X-RAY DIFFRACTION95
2.5765-2.69370.19362560.16664976X-RAY DIFFRACTION95
2.6937-2.83570.1852580.16785011X-RAY DIFFRACTION95
2.8357-3.01320.16282610.16335026X-RAY DIFFRACTION95
3.0132-3.24570.19772550.15745010X-RAY DIFFRACTION95
3.2457-3.57210.16062380.14535061X-RAY DIFFRACTION95
3.5721-4.08830.15432780.14025050X-RAY DIFFRACTION95
4.0883-5.14820.15712770.12635080X-RAY DIFFRACTION95
5.1482-35.11470.16832870.14735224X-RAY DIFFRACTION95

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