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- PDB-6zo1: 1.61 A resolution 3,5-dimethylcatechol (3,5-dimethylbenzene-1,2-d... -

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Basic information

Entry
Database: PDB / ID: 6zo1
Title1.61 A resolution 3,5-dimethylcatechol (3,5-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: 1.61 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)89,75150
Polymers86,3763
Non-polymers3,37547
Water10,215567
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)269,253150
Polymers259,1279
Non-polymers10,126141
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 area71400 Å2
ΔGint-628 kcal/mol
Surface area61480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.566, 131.566, 188.919
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-624-

SO4

21CCC-787-

HOH

31CCC-1010-

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, 614 molecules

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


Mass: 62.068 Da / Num. of mol.: 29 / 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-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.: 567 / 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: 55.45 % / 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationMonochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.61→45.49 Å / Num. obs: 123908 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 21.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.05 / Rrim(I) all: 0.109 / Net I/σ(I): 12.4
Reflection shellResolution: 1.61→1.64 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.659 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6001 / CC1/2: 0.61 / Rpim(I) all: 0.845 / Rrim(I) all: 1.867 / % possible all: 99.6

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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: 1.61→45.49 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.536 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.159 6228 5.027 %
Rwork0.1357 117658 -
all0.137 --
obs-123886 99.637 %
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: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.786 Å20.393 Å20 Å2
2--0.786 Å2-0 Å2
3----2.549 Å2
Refinement stepCycle: LAST / Resolution: 1.61→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 210 567 6818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136594
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176197
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.6578910
X-RAY DIFFRACTIONr_angle_other_deg1.4991.61314423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94122.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.753151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7151540
X-RAY DIFFRACTIONr_chiral_restr0.0980.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021260
X-RAY DIFFRACTIONr_nbd_refined0.2130.21304
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.26033
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23130
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2483
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0870.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.262
X-RAY DIFFRACTIONr_nbd_other0.210.2261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.261
X-RAY DIFFRACTIONr_mcbond_it1.7652.2723296
X-RAY DIFFRACTIONr_mcbond_other1.7652.2723295
X-RAY DIFFRACTIONr_mcangle_it2.4193.3984147
X-RAY DIFFRACTIONr_mcangle_other2.4193.3994148
X-RAY DIFFRACTIONr_scbond_it3.7772.783295
X-RAY DIFFRACTIONr_scbond_other3.2682.6893236
X-RAY DIFFRACTIONr_scangle_it5.2413.994749
X-RAY DIFFRACTIONr_scangle_other4.7193.8494660
X-RAY DIFFRACTIONr_lrange_it6.66428.8977290
X-RAY DIFFRACTIONr_lrange_other6.66428.8957290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6520.2694000.268605X-RAY DIFFRACTION99.6128
1.652-1.6970.244460.248377X-RAY DIFFRACTION99.9887
1.697-1.7460.214420.2078152X-RAY DIFFRACTION99.8954
1.746-1.80.2194280.1937952X-RAY DIFFRACTION99.9285
1.8-1.8590.2084340.1737675X-RAY DIFFRACTION99.9384
1.859-1.9240.1784190.1547420X-RAY DIFFRACTION99.949
1.924-1.9970.1663560.147239X-RAY DIFFRACTION99.9868
1.997-2.0780.1643790.1286933X-RAY DIFFRACTION99.9863
2.078-2.1710.1513320.1186689X-RAY DIFFRACTION99.9573
2.171-2.2770.1553680.1126377X-RAY DIFFRACTION99.8963
2.277-2.40.143290.1076075X-RAY DIFFRACTION99.8908
2.4-2.5450.1532890.1215781X-RAY DIFFRACTION99.7699
2.545-2.7210.1512900.1235403X-RAY DIFFRACTION99.5628
2.721-2.9390.1532590.1235087X-RAY DIFFRACTION99.6087
2.939-3.2190.1592400.1324694X-RAY DIFFRACTION99.5159
3.219-3.5990.1422190.1234250X-RAY DIFFRACTION99.1349
3.599-4.1550.1131970.113764X-RAY DIFFRACTION98.6305
4.155-5.0870.1371730.1083200X-RAY DIFFRACTION98.1951
5.087-7.1870.161450.1492514X-RAY DIFFRACTION97.8293
7.187-80.179830.1761472X-RAY DIFFRACTION95.5747

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