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- PDB-6zo2: 1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-1,2-d... -

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Basic information

Entry
Database: PDB / ID: 6zo2
Title1.65 A resolution 4,5-dimethylcatechol (4,5-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: 1.65 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)89,05641
Polymers86,3763
Non-polymers2,68138
Water11,656647
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)267,169123
Polymers259,1279
Non-polymers8,042114
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 area66960 Å2
ΔGint-558 kcal/mol
Surface area61300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.640, 131.640, 189.254
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-209-

SO4

21AAA-209-

SO4

31CCC-621-

SO4

41CCC-622-

SO4

51CCC-622-

SO4

61CCC-865-

HOH

71CCC-1021-

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, 685 molecules

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


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / 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.: 647 / 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: 2.77 Å3/Da / Density % sol: 55.58 % / 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: 0.96769 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: 0.96769 Å / Relative weight: 1
ReflectionResolution: 1.65→62.245 Å / Num. obs: 116041 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.042 / Rrim(I) all: 0.137 / Net I/σ(I): 18.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 21.2 % / Rmerge(I) obs: 2.811 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5665 / CC1/2: 0.771 / Rpim(I) all: 0.883 / Rrim(I) all: 2.947 / % possible all: 100

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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: 1.65→62.24 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.713 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1556 5813 5.012 %
Rwork0.1344 110166 -
all0.136 --
obs-115979 99.974 %
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: 24.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.729 Å20.365 Å20 Å2
2--0.729 Å20 Å2
3----2.366 Å2
Refinement stepCycle: LAST / Resolution: 1.65→62.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 170 648 6859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176132
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.6538817
X-RAY DIFFRACTIONr_angle_other_deg1.4751.60714269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32522.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.236151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8851540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027343
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021253
X-RAY DIFFRACTIONr_nbd_refined0.2110.21268
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.25924
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23075
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2516
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.259
X-RAY DIFFRACTIONr_nbd_other0.2060.2268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.262
X-RAY DIFFRACTIONr_mcbond_it1.6662.363273
X-RAY DIFFRACTIONr_mcbond_other1.6642.363272
X-RAY DIFFRACTIONr_mcangle_it2.2783.5284113
X-RAY DIFFRACTIONr_mcangle_other2.2783.5284114
X-RAY DIFFRACTIONr_scbond_it3.2612.8043249
X-RAY DIFFRACTIONr_scbond_other3.0152.7443206
X-RAY DIFFRACTIONr_scangle_it4.8194.0444691
X-RAY DIFFRACTIONr_scangle_other4.4033.9494626
X-RAY DIFFRACTIONr_lrange_it6.33829.8287224
X-RAY DIFFRACTIONr_lrange_other6.33829.8367225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.2594200.2518041X-RAY DIFFRACTION99.9764
1.693-1.7390.2374060.2297837X-RAY DIFFRACTION99.9757
1.739-1.790.2323930.217610X-RAY DIFFRACTION99.9875
1.79-1.8450.2044070.1927405X-RAY DIFFRACTION99.9744
1.845-1.9050.2243660.1747211X-RAY DIFFRACTION99.9868
1.905-1.9720.1833500.1596982X-RAY DIFFRACTION100
1.972-2.0460.1693330.1446715X-RAY DIFFRACTION100
2.046-2.130.1633540.1316488X-RAY DIFFRACTION99.9854
2.13-2.2250.1633560.1196192X-RAY DIFFRACTION100
2.225-2.3330.1463310.115966X-RAY DIFFRACTION100
2.333-2.4590.1383000.1135660X-RAY DIFFRACTION99.9162
2.459-2.6080.1452820.1165388X-RAY DIFFRACTION100
2.608-2.7880.1582550.1175101X-RAY DIFFRACTION100
2.788-3.0120.1482320.1174759X-RAY DIFFRACTION99.98
3.012-3.2990.1542550.1314387X-RAY DIFFRACTION99.9569
3.299-3.6880.1331910.1243993X-RAY DIFFRACTION99.9761
3.688-4.2580.122060.1093550X-RAY DIFFRACTION100
4.258-5.2130.121800.1073021X-RAY DIFFRACTION100
5.213-7.3640.1591190.1472429X-RAY DIFFRACTION100
7.364-80.168771431X-RAY DIFFRACTION99.2105

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