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- PDB-7p7n: X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITE... -

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Basic information

Entry
Database: PDB / ID: 7p7n
TitleX-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-PHOSPHINE COMPOUND Au(PEt3)I DETERMINED AT 1.80 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: 1.8 Å
AuthorsMazzei, L. / Ciurli, S.
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)89,92140
Polymers86,2403
Non-polymers3,68137
Water9,872548
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
  • 270 kDa, 9 polymers
Theoretical massNumber of molelcules
Total (without water)269,762120
Polymers258,7199
Non-polymers11,044111
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 area66000 Å2
ΔGint-817 kcal/mol
Surface area58590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.645, 131.645, 189.200
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-611-

AU

21CCC-625-

SO4

31CCC-625-

SO4

41CCC-798-

HOH

51CCC-804-

HOH

61CCC-1059-

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 , 7 types, 585 molecules

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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / 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.: 1 / Source method: obtained synthetically / Formula: C6H15AuP
#9: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Au
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.77 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(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→114 Å / Num. obs: 89759 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 25.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.042 / Rrim(I) all: 0.154 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4534 / CC1/2: 0.694 / Rpim(I) all: 0.931 / Rrim(I) all: 2.484 / % 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: 1.8→72.907 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.15 / WRfactor Rwork: 0.131 / SU B: 2.666 / SU ML: 0.075 / Average fsc free: 0.918 / Average fsc work: 0.9231 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1763 4419 4.926 %
Rwork0.155 85285 -
all0.156 --
obs-89704 99.975 %
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: 31.017 Å2
Baniso -1Baniso -2Baniso -3
1-1.002 Å20.501 Å20 Å2
2--1.002 Å2-0 Å2
3----3.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→72.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 143 549 6686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0126487
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.6448785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61723.25320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.048151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9461537
X-RAY DIFFRACTIONr_chiral_restr0.1160.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024935
X-RAY DIFFRACTIONr_nbd_refined0.2160.23121
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2536
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.2242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.296
X-RAY DIFFRACTIONr_mcbond_it2.4222.8033288
X-RAY DIFFRACTIONr_mcangle_it3.0334.1834152
X-RAY DIFFRACTIONr_scbond_it4.443286.9793197
X-RAY DIFFRACTIONr_scangle_it5.9454.6324632
X-RAY DIFFRACTIONr_lrange_it7.79240.7399898
X-RAY DIFFRACTIONr_rigid_bond_restr21.78537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2973370.2836177X-RAY DIFFRACTION99.954
1.847-1.8970.2663180.2536062X-RAY DIFFRACTION99.9687
1.897-1.9520.2553180.2425876X-RAY DIFFRACTION99.9677
1.952-2.0120.2352840.2235744X-RAY DIFFRACTION99.9668
2.012-2.0780.2182780.1935558X-RAY DIFFRACTION100
2.078-2.1510.2192610.1745419X-RAY DIFFRACTION99.9824
2.151-2.2330.1742750.1575203X-RAY DIFFRACTION100
2.233-2.3240.1862570.1474982X-RAY DIFFRACTION100
2.324-2.4270.1822330.1444864X-RAY DIFFRACTION100
2.427-2.5450.1662500.1434586X-RAY DIFFRACTION99.9793
2.545-2.6830.1752220.144415X-RAY DIFFRACTION100
2.683-2.8460.172210.1334174X-RAY DIFFRACTION100
2.846-3.0420.1552100.143924X-RAY DIFFRACTION99.9758
3.042-3.2860.162060.1413662X-RAY DIFFRACTION99.9742
3.286-3.60.1571800.1353398X-RAY DIFFRACTION100
3.6-4.0240.1551490.1273111X-RAY DIFFRACTION100
4.024-4.6460.1371300.1162770X-RAY DIFFRACTION100
4.646-5.690.1291190.1282372X-RAY DIFFRACTION99.9599
5.69-8.0430.1931020.1571871X-RAY DIFFRACTION100
8.043-72.90.156690.1941117X-RAY DIFFRACTION99.33

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