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- PDB-1y7l: O-Acetylserine Sulfhydrylase Complex -

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Basic information

Entry
Database: PDB / ID: 1y7l
TitleO-Acetylserine Sulfhydrylase Complex
Components
  • O-acetylserine sulfhydrylase
  • decamer fragment of Serine acetyltransferase
KeywordsTRANSFERASE / x-ray crystallography / Sulfhydrylase
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process from serine / cytosol / cytoplasm
Similarity search - Function
Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. ...Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / 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 acetyltransferase / Cysteine synthase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHuang, B. / Vetting, M.W. / Roderick, S.L.
CitationJournal: J.Bacteriol. / Year: 2005
Title: The active site of O-acetylserine sulfhydrylase is the anchor point for bienzyme complex formation with serine acetyltransferase.
Authors: Huang, B. / Vetting, M.W. / Roderick, S.L.
History
DepositionDec 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Nov 15, 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

Downloads & links

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Assembly

Deposited unit
A: O-acetylserine sulfhydrylase
P: decamer fragment of Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8093
Polymers34,7132
Non-polymers961
Water4,450247
1
A: O-acetylserine sulfhydrylase
P: decamer fragment of Serine acetyltransferase
hetero molecules

A: O-acetylserine sulfhydrylase
P: decamer fragment of Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6176
Polymers69,4254
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Unit cell
Length a, b, c (Å)112.569, 112.569, 45.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Cell settingtetragonal
Space group name H-MI41
DetailsThe biological unit is a dimer. The second subunit is generated by the two fold axis: -x,-y,z

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Components

#1: Protein O-acetylserine sulfhydrylase / E.C.2.5.1.47 / Cysteine synthase / O-acetylserine (Thiol)-lyase / CSase


Mass: 33651.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: cysk / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase
#2: Protein/peptide decamer fragment of Serine acetyltransferase / SAT fragment / E.C.2.3.1.30


Mass: 1061.169 Da / Num. of mol.: 1 / Fragment: residues 258-267 / Source method: obtained synthetically
Details: sequence occurs natuarally in Haemophilus influenzae, gene cysE
References: UniProt: P43886
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 26, 2004 / Details: Osmic Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→20.21 Å / Num. all: 40063 / Num. obs: 40063 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.55→1.65 Å / Num. unique all: 5784 / % possible all: 88.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAS

1oas


Resolution: 1.55→20.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1779277.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2031 5.1 %RANDOM
Rwork0.197 ---
all0.204 40060 --
obs0.1971 40060 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6721 Å2 / ksol: 0.408854 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---1.27 Å20 Å2
3---2.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→20.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 5 247 2601
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it0.951.5
X-RAY DIFFRACTIONc_mcangle_it1.292
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 341 5.6 %
Rwork0.29 5784 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4KPL.PARKPL.TOP

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