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- PDB-1d6s: CRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYL... -

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Basic information

Entry
Database: PDB / ID: 1d6s
TitleCRYSTAL STRUCTURE OF THE K41A MUTANT OF O-ACETYLSERINE SULFHYDRYLASE COMPLEXED IN EXTERNAL ALDIMINE LINKAGE WITH METHIONINE
ComponentsO-ACETYLSERINE SULFHYDRYLASE
KeywordsLYASE / CYSTEINE BIOSYNTHESIS / BETA REPLACEMENT ENZYME / PLP / K41A
Function / homology
Function and homology information


cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / 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 / PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase A / Cysteine synthase A
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBurkhard, P. / Tai, C.H. / Ristroph, C.M. / Cook, P.F. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Ligand binding induces a large conformational change in O-acetylserine sulfhydrylase from Salmonella typhimurium.
Authors: Burkhard, P. / Tai, C.H. / Ristroph, C.M. / Cook, P.F. / Jansonius, J.N.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Three-dimensional Structure of O-Acetylserine Sulfhydrylase from Salmonella typhimurium
Authors: Burkhard, P. / Rao, G.S. / Hohenester, E. / Schnackerz, K.D. / Cook, P.F. / Jansonius, J.N.
History
DepositionOct 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-ACETYLSERINE SULFHYDRYLASE
B: O-ACETYLSERINE SULFHYDRYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6176
Polymers68,8252
Non-polymers7934
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-24 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.940, 149.930, 53.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein O-ACETYLSERINE SULFHYDRYLASE


Mass: 34412.320 Da / Num. of mol.: 2 / Mutation: K41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: DW378 / Production host: Escherichia coli (E. coli)
References: UniProt: P12674, UniProt: P0A1E3*PLUS, EC: 4.2.99.8
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30 % PEG 4000 8 % ETHANOL 100 MM TRIS (PH 7.0) 150 MM LI2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %(w/v)PEG40001reservoir
28 %(v/v)ethanol1reservoir
30.1 MTris-HCl1reservoir
40.15 M1reservoirLi2SO4
520.0 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.105
Reflection
*PLUS
Num. all: 32531

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.3→29.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2355706.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1600 5 %RANDOM
Rwork0.174 ---
obs0.174 32175 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.3 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.3 Å20 Å20 Å2
2---4.79 Å20 Å2
3---15.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 48 233 5115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.52
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 173 5.2 %
Rwork0.268 3185 -
obs--57.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PARAM.PLP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.52
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.268

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