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- PDB-1fcj: CRYSTAL STRUCTURE OF OASS COMPLEXED WITH CHLORIDE AND SULFATE -

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Basic information

Entry
Database: PDB / ID: 1fcj
TitleCRYSTAL STRUCTURE OF OASS COMPLEXED WITH CHLORIDE AND SULFATE
ComponentsO-ACETYLSERINE SULFHYDRYLASE
KeywordsLYASE / homodimer
Function / homology
Function and homology information


L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase A
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBurkhard, P. / Tai, C. / Jansonius, J.N. / Cook, P.F.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Identification of an allosteric anion-binding site on O-acetylserine sulfhydrylase: structure of the enzyme with chloride bound.
Authors: Burkhard, P. / Tai, C.H. / Jansonius, J.N. / Cook, P.F.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Lingand binding induces a large conformational change in O-acetylserine sulfhydrylase from salmonella typhimurium
Authors: Burkhard, P. / Tai, C. / Ristroph, C.M. / Cook, P.F. / Jansonius, J.N.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Three-dimensional structure of O-acetylserine sulfhydrylase from salmonella typhimurium
Authors: Burkhard, P. / Jagannatha Rao, G.S. / Hohenester, E. / Schnackerz, K.D. / Cook, P.F. / Jansonius, J.N.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,39616
Polymers137,8824
Non-polymers1,51512
Water20,1411118
1
A: O-ACETYLSERINE SULFHYDRYLASE
C: O-ACETYLSERINE SULFHYDRYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6988
Polymers68,9412
Non-polymers7576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-74 kcal/mol
Surface area22830 Å2
MethodPISA
2
B: O-ACETYLSERINE SULFHYDRYLASE
D: O-ACETYLSERINE SULFHYDRYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6988
Polymers68,9412
Non-polymers7576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-71 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.380, 100.490, 142.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
O-ACETYLSERINE SULFHYDRYLASE / CYSTEINE SYNTHASE A / O-ACETYLSERINE (THIOL)-LYASE A / CSASE A


Mass: 34470.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: P0A1E3, EC: 4.2.99.8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: Peg 4000, Tris-HCl, lithium sulfate, DMSO, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 MTris-HCl1reservoir
40.18 M1reservoirLiSO4
55 %(v/v)DMSO1reservoir

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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: Jan 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 16.7 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 84421 / % possible obs: 89.6 % / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 85.3 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→28.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2867402.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4252 5 %RANDOM
Rwork0.2 ---
obs0.2 84421 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.886 Å2 / ksol: 0.369876 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.27 Å20 Å20 Å2
2--1.9 Å20 Å2
3---4.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9044 0 84 1118 10246
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.044
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.583
X-RAY DIFFRACTIONc_mcangle_it5.14
X-RAY DIFFRACTIONc_scbond_it5.423.5
X-RAY DIFFRACTIONc_scangle_it6.554.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 714 5 %
Rwork0.24 13529 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.622
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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