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- PDB-3zei: Structure of the Mycobacterium tuberculosis O-Acetylserine Sulfhy... -

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Basic information

Entry
Database: PDB / ID: 3zei
TitleStructure of the Mycobacterium tuberculosis O-Acetylserine Sulfhydrylase (OASS) CysK1 in complex with a small molecule inhibitor
ComponentsO-ACETYLSERINE SULFHYDRYLASE
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


Cysteine synthesis from O-acetylserine / cysteine synthase / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AWH / PYRIDOXAL-5'-PHOSPHATE / O-acetylserine sulfhydrylase / O-acetylserine sulfhydrylase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPoyraz, O. / Schnell, R. / Schneider, G.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structure-Guided Design of Novel Thiazolidine Inhibitors of O-Acetyl Serine Sulfhydrylase from Mycobacterium Tuberculosis.
Authors: Poyraz, O. / Jeankumar, V.U. / Saxena, S. / Schnell, R. / Haraldsson, M. / Yogeeswari, P. / Sriram, D. / Schneider, G.
History
DepositionDec 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6825
Polymers32,7861
Non-polymers8964
Water1,72996
1
A: O-ACETYLSERINE SULFHYDRYLASE
hetero molecules

A: O-ACETYLSERINE SULFHYDRYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,36310
Polymers65,5712
Non-polymers1,7928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6570 Å2
ΔGint-64.1 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.820, 71.820, 179.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein O-ACETYLSERINE SULFHYDRYLASE / OAS SULFHYDRYLASE / OASS / CYSTEINE SYNTHASE A / CSASE A / O-ACETYLSERINE (THIOL)-LYASE A / OAS-TL ...OAS SULFHYDRYLASE / OASS / CYSTEINE SYNTHASE A / CSASE A / O-ACETYLSERINE (THIOL)-LYASE A / OAS-TL A / O-ACETYLSERINE-SPECIFIC CYSTEINE SYNTHASE / SULFIDE-DEPENDENT CYSTEINE SYNTHASE


Mass: 32785.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0A534, UniProt: P9WP55*PLUS, cysteine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-AWH / 3-[(Z)-[(5Z)-5-[[2-(2-hydroxy-2-oxoethyloxy)phenyl]methylidene]-3-methyl-4-oxidanylidene-1,3-thiazolidin-2-ylidene]amino]benzoic acid / 3-((Z)-((Z)-5-(2(carboxymethoxy)benzylidene)-3-methyl-4-oxothiazolidin-2-ylidene)amino)benzoic acid


Mass: 412.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N2O6S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.54 Å3/Da / Density % sol: 65.24 % / Description: NONE
Crystal growDetails: 100 MM HEPES, PH8.0, 80% MPD

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→56.09 Å / Num. obs: 32556 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q3B

1q3b


Resolution: 2→56.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.971 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23463 1635 5 %RANDOM
Rwork0.2018 ---
obs0.20347 30862 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2→56.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 60 96 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9372.0113195
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2335307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66623.91392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.571521
X-RAY DIFFRACTIONr_chiral_restr0.2120.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211765
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 109 -
Rwork0.3 2242 -
obs--99.79 %

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