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- PDB-3t4p: Crystal structure of O-Acetyl Serine Sulfhydrylase from Leishmani... -

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Basic information

Entry
Database: PDB / ID: 3t4p
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase from Leishmania donovani in complex with designed tetrapeptide
Components
  • O-acetyl serine sulfhydrylase
  • tetrapeptide DWSI
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Cysteine Synthase / The tryptophan synthase family (fold type II) / Serine acetyl transferase / sulfhydrylase / sulfhydrylase-inhibitor complex / peptide-OASS complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / O-acetyl serine sulfhydrylase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.77 Å
AuthorsRaj, I. / Gourinath, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases with a range of C-terminal sequences
Authors: Raj, I. / Kumar, S. / Gourinath, S.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-acetyl serine sulfhydrylase
B: tetrapeptide DWSI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5684
Polymers36,4272
Non-polymers1422
Water2,990166
1
A: O-acetyl serine sulfhydrylase
B: tetrapeptide DWSI
hetero molecules

A: O-acetyl serine sulfhydrylase
B: tetrapeptide DWSI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1378
Polymers72,8544
Non-polymers2834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7840 Å2
ΔGint-64 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.300, 61.930, 43.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-574-

HOH

31A-651-

HOH

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Components

#1: Protein O-acetyl serine sulfhydrylase


Mass: 35907.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: MHOM/IM/1983/AG83 / Gene: ldOASS, OASS / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1C2I2, cysteine synthase
#2: Protein/peptide tetrapeptide DWSI


Mass: 519.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide synthesis-GenproBiotech
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: KSCN, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 29549 / % possible obs: 97.9 % / Observed criterion σ(F): 5.6 / Observed criterion σ(I): 30.15 / Redundancy: 6.9 % / Rsym value: 0.074 / Net I/σ(I): 9.9
Reflection shellResolution: 1.772→1.818 Å / Redundancy: 4 % / Rmerge(I) obs: 0.426 / % possible all: 77.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å42.2 Å
Translation1.95 Å42.2 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SPX

3spx


Resolution: 1.77→34.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.02 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1213 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20815 1527 4.9 %RANDOM
Rwork0.17686 ---
obs0.17839 29394 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.77→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 8 166 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3251.993346
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06424.49489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38715430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9141513
X-RAY DIFFRACTIONr_chiral_restr0.1920.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211808
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5031.51599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.46322571
X-RAY DIFFRACTIONr_scbond_it4.1443874
X-RAY DIFFRACTIONr_scangle_it6.5344.5775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.772→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 109 -
Rwork0.252 2144 -
obs--99.6 %

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