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- PDB-6zo0: 2.23 A resolution 3,4-dimethylcatechol (3,4-dimethylbenzene-1,2-d... -

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Basic information

Entry
Database: PDB / ID: 6zo0
Title2.23 A resolution 3,4-dimethylcatechol (3,4-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: 2.23 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)88,74237
Polymers86,3783
Non-polymers2,36434
Water7,062392
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)266,227111
Polymers259,1339
Non-polymers7,093102
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 area64680 Å2
ΔGint-409 kcal/mol
Surface area61360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.501, 131.501, 188.710
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-625-

SO4

31CCC-734-

HOH

41CCC-844-

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: 61713.812 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, 426 molecules

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


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: isolated from a natural source / 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.: 392 / 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: 2.75 Å3/Da / Density % sol: 55.36 % / 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: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationMonochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→188.71 Å / Num. obs: 47585 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.125 / Rrim(I) all: 0.299 / Net I/σ(I): 9
Reflection shellResolution: 2.23→2.3 Å / Redundancy: 11 % / Rmerge(I) obs: 1.751 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4300 / CC1/2: 0.657 / Rpim(I) all: 0.804 / Rrim(I) all: 1.929 / % 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: 2.23→113.883 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.124 / SU B: 7.2 / SU ML: 0.163 / Average fsc free: 0.8889 / Average fsc work: 0.9054 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2162 2279 4.794 %
Rwork0.1611 45257 -
all0.164 --
obs-47536 99.971 %
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: 34.357 Å2
Baniso -1Baniso -2Baniso -3
1-1.038 Å20.519 Å20 Å2
2--1.038 Å20 Å2
3----3.368 Å2
Refinement stepCycle: LAST / Resolution: 2.23→113.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 152 394 6587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126481
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.6518760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.575837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1622.975326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.035151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5951540
X-RAY DIFFRACTIONr_chiral_restr0.1220.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024926
X-RAY DIFFRACTIONr_nbd_refined0.2270.23270
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2452
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.2262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.260
X-RAY DIFFRACTIONr_mcbond_it2.7573.1723261
X-RAY DIFFRACTIONr_mcangle_it3.8084.7294095
X-RAY DIFFRACTIONr_scbond_it4.5623.5353219
X-RAY DIFFRACTIONr_scangle_it6.2995.1674652
X-RAY DIFFRACTIONr_lrange_it9.21644.6510005
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
2.23-2.2880.3251580.29332610.29434240.6850.72199.8540.268
2.288-2.3510.3031830.25731960.25933800.7830.81499.97040.23
2.351-2.4190.2711570.23631090.23832660.8420.8431000.207
2.419-2.4930.271360.22730380.22831740.8540.8561000.195
2.493-2.5750.2981610.22129440.22531050.8550.8671000.19
2.575-2.6650.2641400.20128420.20329820.8790.91000.165
2.665-2.7660.2351330.18627600.18828930.9130.9191000.15
2.766-2.8790.291430.18826430.19327860.8780.9171000.152
2.879-3.0060.2221190.17625650.17826850.9240.93499.96280.141
3.006-3.1530.231250.16524430.16825680.9270.9451000.134
3.153-3.3240.2211250.14923280.15324530.9390.9571000.119
3.324-3.5250.2071100.13522210.13823310.9410.9661000.112
3.525-3.7680.1751020.12121050.12422070.9640.9761000.105
3.768-4.070.1681050.11319370.11620420.9710.9811000.1
4.07-4.4570.147900.11618130.11719030.9760.981000.102
4.457-4.9830.153790.11116630.11317420.9750.9811000.095
4.983-5.7520.177670.12714860.12915530.9720.9761000.102
5.752-7.040.171630.12112660.12313290.9720.9811000.1
7.04-9.9370.19560.11510110.11810670.9640.9841000.1
9.937-113.8830.233270.2086260.2096600.9630.96398.93940.197

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