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- PDB-4jbl: Crystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba... -

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Basic information

Entry
Database: PDB / ID: 4jbl
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase from Entamoeba histolytica in complex with Methionine
ComponentsCysteine synthase
KeywordsTRANSFERASE / Cysteine Synthase / substrate analog / PLP fold type 2 / lyase / sulfhydrylase / serine acetyl transferase
Function / homology
Function and homology information


cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE / Cysteine synthase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRaj, I. / Gourinath, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Molecular basis of ligand recognition by OASS from E. histolytica: insights from structural and molecular dynamics simulation studies
Authors: Raj, I. / Mazumder, M. / Gourinath, S.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,8915
Polymers74,5502
Non-polymers3413
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-60 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.417, 80.417, 112.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Cysteine synthase / / O-Acetyl Serine Sulfhydrylase


Mass: 37274.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhOASS / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15570, cysteine synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Details: HIMEDIA CHEMICALS
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2.1M AmSO4, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 30, 2008
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→80.3 Å / Num. all: 46957 / Num. obs: 46902 / % possible obs: 96.8 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 5.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
AUTOMARdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQM

2pqm


Resolution: 2→28.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.612 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 2334 5 %RANDOM
Rwork0.1785 ---
all0.212 ---
obs0.1807 44578 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.01 Å2 / Biso mean: 26.4954 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5181 0 19 329 5529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195262
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.9877098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8665672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43525.423201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51915963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131519
X-RAY DIFFRACTIONr_chiral_restr0.1450.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213835
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 165 -
Rwork0.212 3100 -
all-3265 -
obs--95.41 %

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