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- PDB-6z4n: CRYSTAL STRUCTURE OF OASS COMPLEXED WITH UPAR INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 6z4n
TitleCRYSTAL STRUCTURE OF OASS COMPLEXED WITH UPAR INHIBITOR
ComponentsCysteine synthase A
KeywordsLYASE / CYSTEIN BIOSYNTHESIS / BETA REPLACEMENT ENZYME / PLP DEPENDENT ENZYME / HOMODIMER / INHIBITOR
Function / homology
Function and homology information


cysteine synthase / L-cysteine desulfhydrase activity / 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. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / Chem-Q7B / Cysteine synthase A
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDemitri, N. / Storici, P. / Campanini, B.
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Investigational Studies on a Hit Compound Cyclopropane-Carboxylic Acid Derivative Targeting O -Acetylserine Sulfhydrylase as a Colistin Adjuvant.
Authors: Annunziato, G. / Spadini, C. / Franko, N. / Storici, P. / Demitri, N. / Pieroni, M. / Flisi, S. / Rosati, L. / Iannarelli, M. / Marchetti, M. / Magalhaes, J. / Bettati, S. / Mozzarelli, A. / ...Authors: Annunziato, G. / Spadini, C. / Franko, N. / Storici, P. / Demitri, N. / Pieroni, M. / Flisi, S. / Rosati, L. / Iannarelli, M. / Marchetti, M. / Magalhaes, J. / Bettati, S. / Mozzarelli, A. / Cabassi, C.S. / Campanini, B. / Costantino, G.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Cysteine synthase A
BBB: Cysteine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,00813
Polymers69,4252
Non-polymers1,58311
Water15,655869
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-29 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.261, 96.275, 140.835
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB) / NCS ensembles : (Details: Chains AAA BBB)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Cysteine synthase A / CSase A / O-acetylserine (thiol)-lyase A / OAS-TL A / O-acetylserine sulfhydrylase A


Mass: 34712.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: cysK, STM2430 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1E3, cysteine synthase

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Non-polymers , 6 types, 880 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-Q7B / (1~{S},2~{S})-1-[(4-methylphenyl)methyl]-2-phenyl-cyclopropane-1-carboxylic acid


Mass: 266.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Description: Crystals grew within 5 days at 25C as monoclinic plates of 1.1 mm x 0.4 mm x 0.1 mm dimension. The crystals were soaked for 2 hours at RT in a solution containing 1mM UPAR, 32% (w/v) PEG ...Description: Crystals grew within 5 days at 25C as monoclinic plates of 1.1 mm x 0.4 mm x 0.1 mm dimension. The crystals were soaked for 2 hours at RT in a solution containing 1mM UPAR, 32% (w/v) PEG 4000, 150mM LiSO4, 100 mM Tris pH 7.0 and 5% glycerol (as cryoprotectant agent) and subsequently flash-frozen in N2(l) to be measured.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Drops contained 1 uL of 20 mg/mL StOASS-A mixed with 1 uL of reservoir solution containing 30-31% (w/v) PEG4000, 130-180 mM Li2SO4 (Fluka), 100 mM Tris base pH = 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 25, 2018
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→46.648 Å / Num. obs: 214538 / % possible obs: 94.35 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.08 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0286 / Rpim(I) all: 0.0286 / Rrim(I) all: 0.04044 / Net I/σ(I): 10.89
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.5601 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 14933 / CC1/2: 0.569 / CC star: 0.852 / Rpim(I) all: 0.5601 / Rrim(I) all: 0.7921 / % possible all: 65.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAS

1oas


Resolution: 1.2→46.648 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.116 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1787 10659 4.968 %
Rwork0.1542 203877 -
all0.155 --
obs-214536 94.96 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.685 Å2-0 Å20 Å2
2--2.071 Å2-0 Å2
3----0.387 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 99 869 5755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135375
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175302
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6597309
X-RAY DIFFRACTIONr_angle_other_deg1.5741.58712379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55723.077234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.585151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.491531
X-RAY DIFFRACTIONr_chiral_restr0.1050.2743
X-RAY DIFFRACTIONr_chiral_restr_other1.9310.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025971
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021002
X-RAY DIFFRACTIONr_nbd_refined0.2210.21060
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.25019
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22561
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2461
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.6090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0740.212
X-RAY DIFFRACTIONr_nbd_other0.1730.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.230
X-RAY DIFFRACTIONr_mcbond_it1.4571.5082708
X-RAY DIFFRACTIONr_mcbond_other1.4551.5082707
X-RAY DIFFRACTIONr_mcangle_it1.8892.2783407
X-RAY DIFFRACTIONr_mcangle_other1.892.2793408
X-RAY DIFFRACTIONr_scbond_it2.3241.7842667
X-RAY DIFFRACTIONr_scbond_other2.3161.7842667
X-RAY DIFFRACTIONr_scangle_it2.6742.5643859
X-RAY DIFFRACTIONr_scangle_other2.6742.5653860
X-RAY DIFFRACTIONr_lrange_it3.26818.7316108
X-RAY DIFFRACTIONr_lrange_other2.97418.4265987
X-RAY DIFFRACTIONr_rigid_bond_restr6.148310677
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.0510107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.3185300.31410051X-RAY DIFFRACTION63.8756
1.231-1.2650.3136320.29612294X-RAY DIFFRACTION79.8098
1.265-1.3020.2686650.26813514X-RAY DIFFRACTION90.6006
1.302-1.3420.257260.23914190X-RAY DIFFRACTION97.5923
1.342-1.3860.2277440.20913949X-RAY DIFFRACTION99.6068
1.386-1.4340.2167000.19413636X-RAY DIFFRACTION99.7426
1.434-1.4880.2147300.17613074X-RAY DIFFRACTION99.7759
1.488-1.5490.1966780.16612617X-RAY DIFFRACTION99.8873
1.549-1.6180.1866070.14912180X-RAY DIFFRACTION99.8516
1.618-1.6970.1735550.13511660X-RAY DIFFRACTION99.9264
1.697-1.7890.1895970.13711044X-RAY DIFFRACTION99.9142
1.789-1.8970.1735320.12910539X-RAY DIFFRACTION99.8737
1.897-2.0280.165600.1289805X-RAY DIFFRACTION99.769
2.028-2.190.1484470.129226X-RAY DIFFRACTION99.7216
2.19-2.3990.144290.1158519X-RAY DIFFRACTION99.7992
2.399-2.6820.1454160.1067739X-RAY DIFFRACTION99.951
2.682-3.0960.1393700.126818X-RAY DIFFRACTION99.8611
3.096-3.7910.1583390.145811X-RAY DIFFRACTION99.9025
3.791-5.3550.1522520.1524569X-RAY DIFFRACTION99.855
5.355-46.6480.2871500.2752642X-RAY DIFFRACTION99.8212

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