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- PDB-3tbh: Crystal structure of O-Acetyl Serine Sulfhydrylase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3tbh
TitleCrystal structure of O-Acetyl Serine Sulfhydrylase in complex with octapeptide derived from Serine Acetyl Transferase of Leishmania donovani
Components
  • O-acetyl serine sulfhydrylase
  • Serine acetyl transferase derived octapeptide
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Cysteine Synthase / Type II PLP dependent enzyme / Serine acetyl transferase / Tryptophan synthase beta subunit-like PLP-dependent enzymes / sulfhydrylase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Rossmann fold - #1100 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Trimeric LpxA-like superfamily ...Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Rossmann fold - #1100 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Trimeric LpxA-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine O-acetyltransferase / O-acetyl serine sulfhydrylase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsRaj, I. / Gourinath, S.
CitationJournal: To be Published
Title: Crystal structure of O-Acetyl Serine Sulfhydrylase in complex with octapeptide derived from Serine Acetyl Transferase of Leishmania donovani
Authors: Raj, I. / Kumar, S. / Gourinath, S.
History
DepositionAug 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 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: Serine acetyl transferase derived octapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7773
Polymers36,7542
Non-polymers231
Water3,837213
1
A: O-acetyl serine sulfhydrylase
B: Serine acetyl transferase derived octapeptide
hetero molecules

A: O-acetyl serine sulfhydrylase
B: Serine acetyl transferase derived octapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5546
Polymers73,5084
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6110 Å2
ΔGint-54 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.217, 62.440, 43.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-458-

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 Serine acetyl transferase derived octapeptide


Mass: 846.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Leishmania donovani (eukaryote) / References: UniProt: E9BR69*PLUS
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENTITY 2 IS A OCTAPEPTIDE DERIVED FROM C-TERMINAL OF SERINE ACETYL TRANSFERASE FROM LEISHMANIA DONOVANI.

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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: 42.31 %
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: MARRESEARCH / Detector: CCD / Date: Oct 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.68→115.22 Å / Num. obs: 36632 / % possible obs: 99.59 % / Observed criterion σ(F): 7.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å42.34 Å
Translation1.9 Å42.34 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SPX

3spx


Resolution: 1.68→115.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.1843 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8638 / SU B: 1.773 / SU ML: 0.061 / SU R Cruickshank DPI: 0.104 / SU Rfree: 0.1036 / Cross valid method: THROUGHOUT / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1798 4.9 %RANDOM
Rwork0.1847 ---
obs0.1864 36490 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.53 Å2 / Biso mean: 21.7077 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2--0.26 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.68→115.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 1 213 2617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222447
X-RAY DIFFRACTIONr_angle_refined_deg2.4781.9893315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72524.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.31513
X-RAY DIFFRACTIONr_chiral_restr0.1830.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211802
X-RAY DIFFRACTIONr_mcbond_it1.5891.51600
X-RAY DIFFRACTIONr_mcangle_it2.53922567
X-RAY DIFFRACTIONr_scbond_it3.9793847
X-RAY DIFFRACTIONr_scangle_it6.1594.5747
LS refinement shellResolution: 1.681→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 126 -
Rwork0.25 2470 -
all-2596 -
obs--98.56 %

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