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- PDB-6zo3: 1.55 A resolution 3,6-dimethylcatechol (3,6-dimethylbenzene-1,2-d... -

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Basic information

Entry
Database: PDB / ID: 6zo3
Title1.55 A resolution 3,6-dimethylcatechol (3,6-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease
Components(Urease subunit ...) x 3
KeywordsMETAL BINDING PROTEIN / urease / nickel / enzyme / inhibitor
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
NICKEL (II) ION / HYDROXIDE ION / Urease subunit gamma / Urease subunit alpha / Urease subunit alpha / Urease subunit beta
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies.
Authors: Mazzei, L. / Contaldo, U. / Musiani, F. / Cianci, M. / Bagnolini, G. / Roberti, M. / Ciurli, S.
History
DepositionJul 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 31, 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: Urease subunit gamma
BBB: Urease subunit beta
CCC: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,32832
Polymers86,3763
Non-polymers1,95229
Water13,637757
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)264,98496
Polymers259,1279
Non-polymers5,85687
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 area61720 Å2
ΔGint-338 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.463, 131.463, 189.067
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-1021-

HOH

21CCC-1073-

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: A0A0H3YGY5, 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: 61711.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria)
References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease

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Non-polymers , 5 types, 786 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.: 6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 757 / 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: 55.42 % / Description: Rice shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 50 mM citrate buffer at pH 6.3, containing 1.6 - 2.0 M ammonium sulfate as a precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 13, 2018
RadiationMonochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.55→48.77 Å / Num. obs: 139215 / % possible obs: 99.9 % / Redundancy: 16 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.046 / Rrim(I) all: 0.135 / Net I/σ(I): 17.8
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 15.6 % / Rmerge(I) obs: 2.145 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6635 / CC1/2: 0.67 / Rpim(I) all: 0.792 / Rrim(I) all: 2.288 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G4H

5g4h


Resolution: 1.55→47.311 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.347 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.156 6983 5.024 %
Rwork0.1355 132023 -
all0.136 --
obs-139006 99.967 %
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: 20.213 Å2
Baniso -1Baniso -2Baniso -3
1-0.681 Å20.34 Å20 Å2
2--0.681 Å2-0 Å2
3----2.209 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 136 758 6928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136504
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176134
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.6538797
X-RAY DIFFRACTIONr_angle_other_deg1.5071.60314276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19922.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.389151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0571540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027357
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021255
X-RAY DIFFRACTIONr_nbd_refined0.2230.21324
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26106
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23116
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.22887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2606
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1050.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.256
X-RAY DIFFRACTIONr_nbd_other0.2070.2268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.276
X-RAY DIFFRACTIONr_mcbond_it1.4081.8853279
X-RAY DIFFRACTIONr_mcbond_other1.4081.8853279
X-RAY DIFFRACTIONr_mcangle_it1.9432.8184120
X-RAY DIFFRACTIONr_mcangle_other1.9432.8194121
X-RAY DIFFRACTIONr_scbond_it2.7232.2243224
X-RAY DIFFRACTIONr_scbond_other2.5812.1973201
X-RAY DIFFRACTIONr_scangle_it4.0373.2074662
X-RAY DIFFRACTIONr_scangle_other3.8273.1654627
X-RAY DIFFRACTIONr_lrange_it5.59224.5937402
X-RAY DIFFRACTIONr_lrange_other5.59224.5997403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.2634990.2559634X-RAY DIFFRACTION99.9507
1.59-1.6340.2464880.249382X-RAY DIFFRACTION100
1.634-1.6810.2354840.2249164X-RAY DIFFRACTION99.9896
1.681-1.7330.2344380.2018896X-RAY DIFFRACTION99.9465
1.733-1.790.1984830.1768571X-RAY DIFFRACTION99.9779
1.79-1.8530.1974580.168345X-RAY DIFFRACTION99.9659
1.853-1.9220.1744110.1438071X-RAY DIFFRACTION99.9882
1.922-2.0010.1584120.1347780X-RAY DIFFRACTION99.9756
2.001-2.090.1374150.127439X-RAY DIFFRACTION100
2.09-2.1920.1483920.1127146X-RAY DIFFRACTION100
2.192-2.310.1223580.1056801X-RAY DIFFRACTION100
2.31-2.450.1293330.1066469X-RAY DIFFRACTION100
2.45-2.620.1473350.1136077X-RAY DIFFRACTION100
2.62-2.8290.1493120.1165660X-RAY DIFFRACTION100
2.829-3.0990.1472420.1235295X-RAY DIFFRACTION100
3.099-3.4650.1422580.1334795X-RAY DIFFRACTION100
3.465-40.1222220.1134254X-RAY DIFFRACTION100
4-4.8970.1181950.1093633X-RAY DIFFRACTION99.9739
4.897-6.920.1751580.1522875X-RAY DIFFRACTION99.967
6.92-80.183860.1661699X-RAY DIFFRACTION98.6188

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