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- PDB-7b59: X-ray crystal structure of Sporosarcina pasteurii urease inhibite... -

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Basic information

Entry
Database: PDB / ID: 7b59
TitleX-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Br determined at 1.63 Angstroms
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease / enzyme / nickel / silver
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
SILVER ION / 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: 1.63 Å
AuthorsMazzei, L. / Cianci, M. / Ciurli, S.
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes.
Authors: Mazzei, L. / Cirri, D. / Cianci, M. / Messori, L. / Ciurli, S.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 2.0Apr 20, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / entity_src_nat ...atom_site / entity_src_nat / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_nat.common_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Jan 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)89,18740
Polymers86,2403
Non-polymers2,94737
Water12,719706
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


Theoretical massNumber of molelcules
Total (without water)267,560120
Polymers258,7199
Non-polymers8,842111
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 area68040 Å2
ΔGint-816 kcal/mol
Surface area58820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.410, 131.410, 189.416
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
11AAA-205-

SO4

21AAA-205-

SO4

31CCC-619-

SO4

41CCC-619-

SO4

51CCC-620-

SO4

61CCC-843-

HOH

71CCC-1030-

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, 743 molecules

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


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / 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-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.76 Å3/Da / Density % sol: 55.41 % / Description: Rice-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: THE PROTEIN-LIGAND (600 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME ...Details: THE PROTEIN-LIGAND (600 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.
PH range: 6.3-6.8

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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 / 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: 1.63→113.8 Å / Num. obs: 119894 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.043 / Rrim(I) all: 0.138 / Net I/σ(I): 19.2
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 18.4 % / Rmerge(I) obs: 4.326 / Mean I/σ(I) obs: 1 / Num. unique obs: 5831 / CC1/2: 0.702 / Rpim(I) all: 1.47 / Rrim(I) all: 4.572 / % possible all: 99.8

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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: 6G48

6g48


Resolution: 1.63→113.8 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.345 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1774 5954 4.97 %
Rwork0.1487 113849 -
all0.15 --
obs-119803 99.882 %
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: 28.432 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.535 Å20 Å2
2--1.07 Å20 Å2
3----3.47 Å2
Refinement stepCycle: LAST / Resolution: 1.63→113.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6047 0 151 706 6904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136469
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176049
X-RAY DIFFRACTIONr_angle_refined_deg1.741.6488767
X-RAY DIFFRACTIONr_angle_other_deg1.4521.59514085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53423.094320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.384151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5211538
X-RAY DIFFRACTIONr_chiral_restr0.090.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021236
X-RAY DIFFRACTIONr_nbd_refined0.2130.21304
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.25868
X-RAY DIFFRACTIONr_nbtor_refined0.160.23027
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2576
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.244
X-RAY DIFFRACTIONr_nbd_other0.1910.2233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.272
X-RAY DIFFRACTIONr_mcbond_it1.9672.7813259
X-RAY DIFFRACTIONr_mcbond_other1.9632.7813258
X-RAY DIFFRACTIONr_mcangle_it2.3484.1634098
X-RAY DIFFRACTIONr_mcangle_other2.3494.1634099
X-RAY DIFFRACTIONr_scbond_it3.5733.1593210
X-RAY DIFFRACTIONr_scbond_other3.2723.0873139
X-RAY DIFFRACTIONr_scangle_it4.9344.6094659
X-RAY DIFFRACTIONr_scangle_other4.5444.54552
X-RAY DIFFRACTIONr_lrange_it5.87236.6817233
X-RAY DIFFRACTIONr_lrange_other5.69536.0227057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.63-1.6720.3294250.33683000.33587500.4230.40199.71430.299
1.672-1.7180.3094600.30480090.30584870.5890.58999.78790.267
1.718-1.7680.2814020.26579040.26683230.7290.75299.79570.224
1.768-1.8220.2564060.23876560.23880750.8070.8299.8390.195
1.822-1.8820.2573670.21574430.21778170.8450.86699.91040.173
1.882-1.9480.2333700.20171940.20375710.8860.89499.90750.157
1.948-2.0220.2033710.17969590.1873330.9240.92899.95910.136
2.022-2.1040.2023640.16266760.16470430.9330.94599.95740.125
2.104-2.1980.1943520.14564350.14867930.950.95999.91170.111
2.198-2.3050.1563280.13261620.13364990.9640.96999.86150.1
2.305-2.430.1693040.12858840.1361930.9610.97299.91930.1
2.43-2.5770.1733090.1355400.13258520.9660.97399.94870.102
2.577-2.7550.1722670.12152500.12455210.9660.97899.92760.098
2.755-2.9750.1682650.12549080.12751750.9670.97799.96130.105
2.975-3.2590.1472200.13645500.13647730.9750.97799.93710.118
3.259-3.6430.161800.13541800.13643620.9760.97999.95420.122
3.643-4.2060.1191970.1136710.11138690.9850.98699.97420.103
4.206-5.150.1441640.10531390.10733040.9810.98799.96970.101
5.15-7.2750.1681300.13224940.13326260.9750.9899.92380.125
7.275-113.8040.169730.16414950.16415780.9740.96899.36630.157

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