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- PDB-5ol4: 1.28 A resolution of Sporosarcina pasteurii urease inhibited in t... -

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Basic information

Entry
Database: PDB / ID: 5ol4
Title1.28 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPT
Components(Urease subunit ...) x 3
KeywordsHYDROLASE / Urease Nickel NBPT enzyme
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit ...Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / 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 / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Ribbon / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphoramidothioic O,O-acid / NICKEL (II) ION / Urease subunit gamma / Urease subunit alpha / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsMazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S.
CitationJournal: Biochemistry / Year: 2017
Title: Urease Inhibition in the Presence of N-(n-Butyl)thiophosphoric Triamide, a Suicide Substrate: Structure and Kinetics.
Authors: Mazzei, L. / Cianci, M. / Contaldo, U. / Musiani, F. / Ciurli, S.
History
DepositionJul 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)87,81326
Polymers86,2403
Non-polymers1,57423
Water14,088782
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)263,44078
Polymers258,7199
Non-polymers4,72169
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
Unit cell
Length a, b, c (Å)131.742, 131.742, 188.930
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-611-

SO4

21C-611-

SO4

31C-1010-

HOH

41C-1150-

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: A0A0H3YGY5, UniProt: P41022*PLUS, 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: A0A0H3YL32, UniProt: P41020*PLUS, urease

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Non-polymers , 5 types, 805 molecules

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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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-9XN / Phosphoramidothioic O,O-acid


Mass: 113.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H4NO2PS / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O

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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: 55.52 % / Description: Rice-shaped crystals
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
PH range: 6.3-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2016
RadiationMonochromator: Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.28→114.09 Å / Num. obs: 243939 / % possible obs: 99.4 % / Redundancy: 14.3 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.033 / Net I/σ(I): 15.9
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 14.6 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 11805 / CC1/2: 0.673 / Rpim(I) all: 0.625 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimless0.2.8data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UBP

3ubp


Resolution: 1.28→114.09 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.352 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13684 12246 5 %RANDOM
Rwork0.11903 ---
obs0.11992 231654 99.26 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 14.901 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å2-0 Å2
2--0.23 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.28→114.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 90 782 6918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196536
X-RAY DIFFRACTIONr_bond_other_d0.0020.026309
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9758853
X-RAY DIFFRACTIONr_angle_other_deg0.808314580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35925.053285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.775151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4061538
X-RAY DIFFRACTIONr_chiral_restr0.0850.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217545
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021384
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_it0.6851.2453332
X-RAY DIFFRACTIONr_mcbond_other0.6851.2443331
X-RAY DIFFRACTIONr_mcangle_it0.9281.8764214
X-RAY DIFFRACTIONr_mcangle_other0.9281.8764215
X-RAY DIFFRACTIONr_scbond_it1.5471.5053203
X-RAY DIFFRACTIONr_scbond_other1.5471.5053204
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9352.1594639
X-RAY DIFFRACTIONr_long_range_B_refined2.56711.9347996
X-RAY DIFFRACTIONr_long_range_B_other2.56711.9377997
X-RAY DIFFRACTIONr_rigid_bond_restr8.153312844
X-RAY DIFFRACTIONr_sphericity_free26.4815178
X-RAY DIFFRACTIONr_sphericity_bonded6.804513337
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 865 -
Rwork0.251 16733 -
obs--97.96 %

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