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- PDB-2q3c: 2.1 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylas... -

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Basic information

Entry
Database: PDB / ID: 2q3c
Title2.1 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylase (OASS) Holoenzyme From MYCOBACTERIUM TUBERCULOSIS in Complex with the Inhibitory Peptide DFSI
Components
  • Cysteine synthase A
  • DFSI inhibitory peptide
KeywordsTRANSFERASE / Mycobacterium tuberculosis / Pyridoxal-5'-phosphate / sulphur metabolism / cysteine biosynthesis / SAT / peptide-inhibitor
Function / homology
Function and homology information


Cysteine synthesis from O-acetylserine / cysteine synthase / L-cysteine desulfhydrase activity / cysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / extracellular region / cytosol / 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
O-acetylserine sulfhydrylase / O-acetylserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchneider, G. / Schnell, R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural Insights into Catalysis and Inhibition of O-Acetylserine Sulfhydrylase from Mycobacterium tuberculosis: CRYSTAL STRUCTURES OF THE ENZYME {alpha}-AMINOACRYLATE INTERMEDIATE AND AN ...Title: Structural Insights into Catalysis and Inhibition of O-Acetylserine Sulfhydrylase from Mycobacterium tuberculosis: CRYSTAL STRUCTURES OF THE ENZYME {alpha}-AMINOACRYLATE INTERMEDIATE AND AN ENZYME-INHIBITOR COMPLEX.
Authors: Schnell, R. / Oehlmann, W. / Singh, M. / Schneider, G.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 2, 2014Group: Source and taxonomy
Revision 1.4Aug 30, 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 1.5Nov 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

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Assembly

Deposited unit
A: Cysteine synthase A
B: DFSI inhibitory peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8953
Polymers33,7772
Non-polymers1181
Water2,936163
1
A: Cysteine synthase A
B: DFSI inhibitory peptide
hetero molecules

A: Cysteine synthase A
B: DFSI inhibitory peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7896
Polymers67,5534
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)72.458, 72.458, 178.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe OASS forms a dimer, the second part of the biological assembly is generated by the two fold axis: -y, x, -z.

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Components

#1: Protein Cysteine synthase A / O-acetylserine sulfhydrylase A / O-acetylserine Thiol / lyase A / CSase A


Mass: 33296.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Rv2334 / Gene: cysK / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A534, UniProt: P9WP55*PLUS, cysteine synthase
#2: Protein/peptide DFSI inhibitory peptide


Mass: 480.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.61 Å3/Da / Density % sol: 65.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPES, 80% MPD, 4 mM DFSI-peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: Diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→59.66 Å / Num. all: 26571 / Num. obs: 26571 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3941 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2Q3B, Holoenzyme

2q3b


Resolution: 2.1→51.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.219 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20747 1341 5.1 %RANDOM
Rwork0.18723 ---
all0.18826 25171 --
obs0.18826 25171 92.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.734 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2--1.94 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 8 163 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222331
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9973173
X-RAY DIFFRACTIONr_angle_other_deg6.9328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8355306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04123.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6141521
X-RAY DIFFRACTIONr_chiral_restr0.130.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021749
X-RAY DIFFRACTIONr_nbd_refined0.1920.21112
X-RAY DIFFRACTIONr_nbd_other0.0930.28
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21617
X-RAY DIFFRACTIONr_nbtor_other0.0470.25
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.211
X-RAY DIFFRACTIONr_mcbond_it0.5871.51558
X-RAY DIFFRACTIONr_mcangle_it1.00222441
X-RAY DIFFRACTIONr_scbond_it1.5883853
X-RAY DIFFRACTIONr_scangle_it2.8184.5730
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 101 -
Rwork0.267 1891 -
obs-3941 95.86 %

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