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- PDB-8biv: Cystathionine gamma-lyase N360S mutant from Toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 8biv
TitleCystathionine gamma-lyase N360S mutant from Toxoplasma gondii
ComponentsCystathionine beta-lyase, putative
KeywordsCYTOSOLIC PROTEIN / transsulfuration pathway / hydrogen sulfide / toxoplasma gondii / N360S mutant
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
PYRIDOXAL-5'-PHOSPHATE / cystathionine gamma-synthase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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
A: Cystathionine beta-lyase, putative
E: Cystathionine beta-lyase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5876
Polymers91,9092
Non-polymers6784
Water4,486249
1
A: Cystathionine beta-lyase, putative
E: Cystathionine beta-lyase, putative
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)185,17512
Polymers183,8184
Non-polymers1,3578
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area27000 Å2
ΔGint-153 kcal/mol
Surface area45390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.738, 157.738, 93.331
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-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 66.27 %
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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.22→93.331 Å / Num. obs: 65911 / % possible obs: 100 % / Redundancy: 30 % / CC1/2: 0.997 / Net I/σ(I): 12.9
Reflection shellResolution: 2.22→2.26 Å / Num. unique obs: 3250 / CC1/2: 0.888

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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: 2.22→93.331 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.263 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21605 3350 5.1 %RANDOM
Rwork0.19451 ---
obs0.19558 62550 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å2-0 Å2
2---0.18 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.22→93.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6109 0 42 249 6400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175836
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.6438628
X-RAY DIFFRACTIONr_angle_other_deg1.1241.56813568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94322.708288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5011528
X-RAY DIFFRACTIONr_chiral_restr0.0440.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021296
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8942.6643209
X-RAY DIFFRACTIONr_mcbond_other0.8942.6643208
X-RAY DIFFRACTIONr_mcangle_it1.6393.994020
X-RAY DIFFRACTIONr_mcangle_other1.6393.9914021
X-RAY DIFFRACTIONr_scbond_it0.7392.7343140
X-RAY DIFFRACTIONr_scbond_other0.7392.7353141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3124.0614609
X-RAY DIFFRACTIONr_long_range_B_refined3.85831.1076984
X-RAY DIFFRACTIONr_long_range_B_other3.82731.0636950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.223→2.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 234 -
Rwork0.229 4570 -
obs--99.9 %

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