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- PDB-7p7o: X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITE... -

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Basic information

Entry
Database: PDB / ID: 7p7o
TitleX-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-DIPHOSPHINE COMPOUND Au(PEt3)2Cl DETERMINED AT 1.87 ANGSTROMS
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease / nickel / gold / enzyme / urea
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, 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
triethylphosphanuidylgold(1+) / NICKEL (II) ION / OXYGEN ATOM / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMazzei, L. / Ciurli, S. / Cianci, M. / Messori, L. / Massai, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dalton Trans / Year: 2021
Title: Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition.
Authors: Mazzei, L. / Massai, L. / Cianci, M. / Messori, L. / Ciurli, S.
History
DepositionJul 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,57835
Polymers86,2403
Non-polymers3,33832
Water8,449469
1
AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules

AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules

AAA: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 269 kDa, 9 polymers
Theoretical massNumber of molelcules
Total (without water)268,734105
Polymers258,7199
Non-polymers10,01596
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 area64770 Å2
ΔGint-1003 kcal/mol
Surface area58620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.797, 131.797, 189.381
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11CCC-614-

SO4

21CCC-621-

SO4

31CCC-621-

SO4

41CCC-825-

HOH

51CCC-844-

HOH

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Components

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Urease subunit ... , 3 types, 3 molecules AAABBBCCC

#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 , 6 types, 501 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / 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-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#8: Chemical ChemComp-AUF / triethylphosphanuidylgold(1+) / gold(I)-triethylphosphane


Mass: 315.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15AuP
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.6 % / Description: rice shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: THE PROTEIN-LIGAND (1.2 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 10% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.2-1.7 M AMMONIUM SULFATE ALSO CONTAINING THE SAME ...Details: THE PROTEIN-LIGAND (1.2 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 10% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.2-1.7 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.

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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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.87→114 Å / Num. obs: 80498 / % possible obs: 100 % / Redundancy: 17.4 % / Biso Wilson estimate: 26.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.038 / Rrim(I) all: 0.159 / Net I/σ(I): 17.9
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 17.5 % / Rmerge(I) obs: 3.098 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4557 / CC1/2: 0.744 / Rpim(I) all: 0.778 / Rrim(I) all: 3.296 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ol4

5ol4


Resolution: 1.87→65.985 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.137 / SU B: 3.947 / SU ML: 0.107 / Average fsc free: 0.8765 / Average fsc work: 0.8915 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2103 4008 4.982 %
Rwork0.165 76434 -
all0.167 --
obs-80442 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.357 Å20.679 Å20 Å2
2--1.357 Å2-0 Å2
3----4.404 Å2
Refinement stepCycle: LAST / Resolution: 1.87→65.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5993 0 150 469 6612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126519
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.6448845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06723.125320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.055151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8891538
X-RAY DIFFRACTIONr_chiral_restr0.1230.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024948
X-RAY DIFFRACTIONr_nbd_refined0.2230.23157
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2478
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.2211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.274
X-RAY DIFFRACTIONr_mcbond_it3.2683.5243294
X-RAY DIFFRACTIONr_mcangle_it3.7865.2564163
X-RAY DIFFRACTIONr_scbond_it5.7623.9233223
X-RAY DIFFRACTIONr_scangle_it7.2855.744681
X-RAY DIFFRACTIONr_lrange_it8.5657704.2679917
X-RAY DIFFRACTIONr_rigid_bond_restr15.674321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.9190.3323060.325569X-RAY DIFFRACTION99.966
1.919-1.9710.3162930.2875417X-RAY DIFFRACTION100
1.971-2.0280.2812930.2595271X-RAY DIFFRACTION99.9641
2.028-2.0910.262590.235131X-RAY DIFFRACTION100
2.091-2.1590.2512540.2074986X-RAY DIFFRACTION99.9428
2.159-2.2350.2322380.1894842X-RAY DIFFRACTION99.9803
2.235-2.3190.2242410.1734658X-RAY DIFFRACTION100
2.319-2.4140.2362300.1734478X-RAY DIFFRACTION99.9788
2.414-2.5210.242280.1654312X-RAY DIFFRACTION100
2.521-2.6440.2082090.164149X-RAY DIFFRACTION100
2.644-2.7870.2382000.1593958X-RAY DIFFRACTION100
2.787-2.9570.2451970.1613727X-RAY DIFFRACTION99.9745
2.957-3.1610.1881830.163539X-RAY DIFFRACTION99.9731
3.161-3.4140.1991880.1533277X-RAY DIFFRACTION100
3.414-3.7390.1921640.1413042X-RAY DIFFRACTION99.9377
3.739-4.1810.1641410.1292783X-RAY DIFFRACTION99.9658
4.181-4.8270.1461230.1172480X-RAY DIFFRACTION99.8083
4.827-5.9110.1751100.1332125X-RAY DIFFRACTION99.9553
5.911-8.3550.1741050.1351668X-RAY DIFFRACTION99.9436
8.355-65.980.254460.1861022X-RAY DIFFRACTION99.2565

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