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- PDB-6kr5: Crystal structure of O-Acetyl Serine Sulfhydrylase isoform 3 from... -

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Basic information

Entry
Database: PDB / ID: 6kr5
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase isoform 3 from Entamoeba histolytica
ComponentsCysteine synthase 3
KeywordsTRANSFERASE / O-acetylserine sulphydralase / Cysteine synthase transferase O-acetyl-L-serine(thiol)lyase
Function / homology
Function and homology information


cysteine synthase / hydrogen sulfide biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase 3
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.544 Å
AuthorsDharavath, S. / Gourinath, S.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Crystal structure of O-Acetylserine sulfhydralase (OASS) isoform 3 from Entamoeba histolytica: Pharmacophore-based virtual screening and validation of novel inhibitors.
Authors: Dharavath, S. / Vijayan, R. / Kumari, K. / Tomar, P. / Gourinath, S.
History
DepositionAug 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase 3
B: Cysteine synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4774
Polymers72,9822
Non-polymers4942
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-46 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.505, 85.874, 91.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine synthase 3 / / Cysteine synthase A / putative / Cysteine synthase a putative


Mass: 36491.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: CS 3, CL6EHI_060340, EHI_060340 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q401L7, cysteine synthase
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.18 Å3/Da / Density % sol: 43.46 % / Description: rod shaped
Crystal growTemperature: 289.15 K / Method: vapor diffusion / Details: 0.1M PCTP buffer, 25% PEG 1500 / PH range: 4.0 - 7.0

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 92112 / % possible obs: 99.5 % / Redundancy: 7.3 % / CC1/2: 0.83 / Rpim(I) all: 0.27 / Rrim(I) all: 0.074 / Χ2: 2.1 / Net I/av σ(I): 2 / Net I/σ(I): 44
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4544 / CC1/2: 0.83 / Rrim(I) all: 0.92 / Χ2: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3352refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQM

2pqm


Resolution: 1.544→29.366 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 1003 1.09 %
Rwork0.1805 90941 -
obs0.1809 91944 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.73 Å2 / Biso mean: 28.4354 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 1.544→29.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 37 704 5743
Biso mean--21.27 35.86 -
Num. residues----670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5444-1.62580.27521310.2261230695
1.6258-1.72760.2231500.19713023100
1.7276-1.8610.21021400.19713056100
1.861-2.04820.25861500.196713038100
2.0482-2.34450.21041410.183613127100
2.3445-2.95340.22881440.19513182100
2.9534-29.30.19771470.16181320997

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