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- PDB-7zcy: Sporosarcina pasteurii urease (SPU) co-crystallized in the presen... -

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Basic information

Entry
Database: PDB / ID: 7zcy
TitleSporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease / nickel / Ebselen / selenium
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit ...Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Chem-IU9 / NICKEL (II) ION / HYDROXIDE ION / SELENIUM ATOM / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsMazzei, L. / Ciurli, S. / Cianci, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: J.Med.Chem. / Year: 2023
Title: Optimized Ebselen-Based Inhibitors of Bacterial Ureases with Nontypical Mode of Action.
Authors: Macegoniuk, K. / Tabor, W. / Mazzei, L. / Cianci, M. / Giurg, M. / Olech, K. / Burda-Grabowska, M. / Kaleta, R. / Grabowiecka, A. / Mucha, A. / Ciurli, S. / Berlicki, L.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,87037
Polymers86,2403
Non-polymers2,63134
Water13,818767
1
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,611111
Polymers258,7199
Non-polymers7,892102
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area65660 Å2
ΔGint-446 kcal/mol
Surface area59820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.612, 131.612, 189.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-608-

SO4

21C-608-

SO4

31C-609-

SO4

41C-1013-

HOH

51C-1026-

HOH

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Components

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Urease subunit ... , 3 types, 3 molecules ABC

#1: Protein Urease subunit gamma / Urea amidohydrolase subunit gamma


Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41022, urease
#2: Protein Urease subunit beta / Urea amidohydrolase subunit beta


Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41021, urease
#3: Protein Urease subunit alpha / Urea amidohydrolase subunit alpha


Mass: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41020, urease

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Non-polymers , 7 types, 801 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#8: Chemical ChemComp-IU9 / N-(2-chloranyl-4-fluoranyl-phenyl)-2-selanyl-benzamide


Mass: 328.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClFNOSe / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-SE / SELENIUM ATOM


Mass: 78.960 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Se
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.72 Å3/Da / Density % sol: 54.9 % / Description: Rice shaped
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.3
Details: Protein-ligand (1 mM ligand concentration) complex in 50 mM HEPES buffer, pH 7.50 (also containing 10% (V/V) DMSO), diluted 1:1 with 1.6-2.1 M ammonium sulfate also containing 100 mM sodium citrate at pH 6.3
PH range: 6.3-6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.54→189 Å / Num. obs: 142031 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 21.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.031 / Rrim(I) all: 0.099 / Net I/σ(I): 20.9
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 19.9 % / Rmerge(I) obs: 2.301 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6976 / CC1/2: 0.749 / Rpim(I) all: 0.752 / Rrim(I) all: 2.422 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4H

5g4h


Resolution: 1.54→97.8 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.359 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15991 7016 4.9 %RANDOM
Rwork0.13747 ---
obs0.13857 134952 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å2-0 Å2
2--0.7 Å2-0 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 1.54→97.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 143 767 6956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136640
X-RAY DIFFRACTIONr_bond_other_d0.0030.0156355
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.6518976
X-RAY DIFFRACTIONr_angle_other_deg1.51.58514692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73522.793333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.928151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2631542
X-RAY DIFFRACTIONr_chiral_restr0.0990.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027718
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021418
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_it1.8442.3923340
X-RAY DIFFRACTIONr_mcbond_other1.8422.3923339
X-RAY DIFFRACTIONr_mcangle_it2.533.584222
X-RAY DIFFRACTIONr_mcangle_other2.533.5814223
X-RAY DIFFRACTIONr_scbond_it3.2372.7893299
X-RAY DIFFRACTIONr_scbond_other3.2342.7883299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5064.0364744
X-RAY DIFFRACTIONr_long_range_B_refined5.92230.3617461
X-RAY DIFFRACTIONr_long_range_B_other5.92330.377462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 512 -
Rwork0.285 9864 -
obs--99.9 %

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