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- PDB-6znz: 1.89 A resolution 4-methylcatechol (4-methylbenzene-1,2-diol) inh... -

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Basic information

Entry
Database: PDB / ID: 6znz
Title1.89 A resolution 4-methylcatechol (4-methylbenzene-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: 1.89 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

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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)89,03742
Polymers86,3623
Non-polymers2,67539
Water10,521584
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)267,110126
Polymers259,0859
Non-polymers8,024117
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 area65860 Å2
ΔGint-395 kcal/mol
Surface area60690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.021, 131.021, 188.879
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-621-

SO4

21CCC-621-

SO4

31CCC-625-

SO4

41CCC-803-

HOH

51CCC-1001-

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: 61697.773 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, 623 molecules

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


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / 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.: 584 / 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: 2.74 Å3/Da / Density % sol: 55.07 % / 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: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationMonochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→97.27 Å / Num. obs: 76691 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.098 / Rrim(I) all: 0.159 / Net I/σ(I): 9.5
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4494 / CC1/2: 0.675 / Rpim(I) all: 0.698 / Rrim(I) all: 1.099 / % possible all: 99.8

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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: 1.89→97.27 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.649 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1781 3779 4.93 %
Rwork0.1591 72877 -
all0.16 --
obs-76656 99.709 %
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: 27.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.181 Å20.591 Å20 Å2
2--1.181 Å20 Å2
3----3.831 Å2
Refinement stepCycle: LAST / Resolution: 1.89→97.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6040 0 171 584 6795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126517
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6498800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2365841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68122.988328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.708151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881540
X-RAY DIFFRACTIONr_chiral_restr0.1050.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024943
X-RAY DIFFRACTIONr_nbd_refined0.2140.23278
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2592
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.2274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.284
X-RAY DIFFRACTIONr_mcbond_it1.9432.4793271
X-RAY DIFFRACTIONr_mcangle_it2.5943.6974111
X-RAY DIFFRACTIONr_scbond_it3.5342.8223245
X-RAY DIFFRACTIONr_scangle_it4.8534.0834676
X-RAY DIFFRACTIONr_lrange_it6.54835.66810184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.9390.3022750.2995301X-RAY DIFFRACTION99.821
1.939-1.9920.2652685191X-RAY DIFFRACTION99.9268
1.992-2.050.2752550.2515047X-RAY DIFFRACTION99.7179
2.05-2.1130.2692290.2624909X-RAY DIFFRACTION99.6509
2.113-2.1820.2142440.2054762X-RAY DIFFRACTION99.8205
2.182-2.2590.1892520.1874586X-RAY DIFFRACTION99.9587
2.259-2.3440.1942160.1734448X-RAY DIFFRACTION99.5305
2.344-2.440.1972270.1674278X-RAY DIFFRACTION100
2.44-2.5480.1852080.1624135X-RAY DIFFRACTION99.908
2.548-2.6730.1922040.1523958X-RAY DIFFRACTION100
2.673-2.8170.1821920.1413740X-RAY DIFFRACTION99.62
2.817-2.9880.1781830.1383596X-RAY DIFFRACTION99.9735
2.988-3.1940.1511850.1413353X-RAY DIFFRACTION99.9435
3.194-3.450.1481730.1333129X-RAY DIFFRACTION99.8186
3.45-3.7780.1551590.1142906X-RAY DIFFRACTION99.9674
3.778-4.2240.1331280.1082650X-RAY DIFFRACTION99.2143
4.224-4.8760.1221320.1032356X-RAY DIFFRACTION99.7594
4.876-5.9690.141110.1272025X-RAY DIFFRACTION99.9532
5.969-8.430.156870.1371581X-RAY DIFFRACTION98.4652
6-80.14851926X-RAY DIFFRACTION94.2141

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