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- PDB-8q2e: The 1.68-A X-ray crystal structure of Sporosarcina pasteurii urea... -

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Basic information

Entry
Database: PDB / ID: 8q2e
TitleThe 1.68-A X-ray crystal structure of Sporosarcina pasteurii urease inhibited by thiram and bound to dimethylditiocarbamate
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / urease / nickel / thiram / dimethyldithiocarbamate / enzyme
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
dimethylcarbamodithioic acid / NICKEL (II) ION / HYDROXIDE ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMazzei, L. / Cianci, M. / Ciurli, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
University of Bologna Italy
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Kinetic and structural details of urease inactivation by thiuram disulphides.
Authors: Mazzei, L. / Paul, A. / Cianci, M. / Devodier, M. / Mandelli, D. / Carloni, P. / Ciurli, S.
History
DepositionAug 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,33644
Polymers86,2403
Non-polymers3,09641
Water9,980554
1
A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules

A: Urease subunit gamma
B: Urease subunit beta
C: Urease subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,007132
Polymers258,7199
Non-polymers9,288123
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 area67840 Å2
ΔGint-682 kcal/mol
Surface area61180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.511, 131.511, 189.017
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-2321-

SO4

21C-2322-

SO4

31C-2322-

SO4

41C-2514-

HOH

51C-2694-

HOH

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Components

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Urease subunit ... , 3 types, 3 molecules ABC

#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: P41022, 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: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41020, urease

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Non-polymers , 6 types, 595 molecules

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


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-IS9 / dimethylcarbamodithioic acid


Mass: 121.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NS2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.72 Å3/Da / Density % sol: 54.86 % / Description: Rice-shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM citrate, pH 6.3, 1.6-2.1 M ammonium sulfate

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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: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.68→114.5 Å / Num. obs: 109674 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.032 / Rrim(I) all: 0.142 / Net I/σ(I): 18.9
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 20.4 % / Rmerge(I) obs: 2.4 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5354 / CC1/2: 0.738 / Rpim(I) all: 0.556 / Rrim(I) all: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→114.15 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.831 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16318 5465 5 %RANDOM
Rwork0.13815 ---
obs0.13942 104151 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.285 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å2-0 Å2
3----3.37 Å2
Refinement stepCycle: 1 / Resolution: 1.68→114.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 162 554 6774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126609
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166320
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.6628941
X-RAY DIFFRACTIONr_angle_other_deg0.5711.5814613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.377542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.967101148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0422.5323312
X-RAY DIFFRACTIONr_mcbond_other2.042.5313311
X-RAY DIFFRACTIONr_mcangle_it2.6674.5364181
X-RAY DIFFRACTIONr_mcangle_other2.6674.5384182
X-RAY DIFFRACTIONr_scbond_it3.9333.0343297
X-RAY DIFFRACTIONr_scbond_other3.4412.9263234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9525.1864654
X-RAY DIFFRACTIONr_long_range_B_refined8.27331.327365
X-RAY DIFFRACTIONr_long_range_B_other8.27331.327364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 424 -
Rwork0.301 7556 -
obs--99.9 %

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