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- PDB-2ubp: STRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII -

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Basic information

Entry
Database: PDB / ID: 2ubp
TitleSTRUCTURE OF NATIVE UREASE FROM BACILLUS PASTEURII
Components(PROTEIN (UREASE ...) x 3
KeywordsHYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL
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
NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBenini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Miletti, S. / Ciurli, S. / Mangani, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and Beta-Mercaptoethanol-Inhibited Urease from Bacillus Pasteurii
Authors: Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S.
#2: Journal: J.Biol.Inorg.Chem. / Year: 1998
Title: The Complex of Bacillus Pasteurii Urease with Beta-Mercaptoethanol from X-Ray Data at 1.65 A Resolution
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
#3: Journal: Soil Biol.Biochem. / Year: 1996
Title: Bacillus Pasteurii Urease: A Heteropolimeric Enzyme with a Binuclear Nickel Active Site
Authors: Benini, S. / Gessa, C. / Ciurli, S.
#4: Journal: Eur.J.Biochem. / Year: 1996
Title: X-Ray Absorption Spectroscopy Study of Native and Phenylphosphorodiamidate- Inhibited Bacillus Pasteurii Urease
Authors: Benini, S. / Ciurli, S. / Nolting, H.F. / Mangani, S.
History
DepositionNov 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 8, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 31, 2023Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 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: PROTEIN (UREASE GAMMA SUBUNIT)
B: PROTEIN (UREASE BETA SUBUNIT)
C: PROTEIN (UREASE ALPHA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5766
Polymers86,3633
Non-polymers2133
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-71 kcal/mol
Surface area30250 Å2
MethodPISA
2
A: PROTEIN (UREASE GAMMA SUBUNIT)
B: PROTEIN (UREASE BETA SUBUNIT)
C: PROTEIN (UREASE ALPHA SUBUNIT)
hetero molecules

A: PROTEIN (UREASE GAMMA SUBUNIT)
B: PROTEIN (UREASE BETA SUBUNIT)
C: PROTEIN (UREASE ALPHA SUBUNIT)
hetero molecules

A: PROTEIN (UREASE GAMMA SUBUNIT)
B: PROTEIN (UREASE BETA SUBUNIT)
C: PROTEIN (UREASE ALPHA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,72918
Polymers259,0899
Non-polymers6409
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 area48870 Å2
ΔGint-349 kcal/mol
Surface area60470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.357, 131.357, 189.756
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-1224-

HOH

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Components

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PROTEIN (UREASE ... , 3 types, 3 molecules ABC

#1: Protein PROTEIN (UREASE GAMMA SUBUNIT) / UREA AMINOHYDROLASE


Mass: 11187.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / Strain: DSM 33 / References: UniProt: P41022, urease
#2: Protein PROTEIN (UREASE BETA SUBUNIT) / UREA AMINOHYDROLASE


Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / Strain: DSM 33 / References: UniProt: P41021, urease
#3: Protein PROTEIN (UREASE ALPHA SUBUNIT) / UREA AMINOHYDROLASE


Mass: 61646.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / Strain: DSM 33 / References: UniProt: P41020, urease

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Non-polymers , 3 types, 884 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 881 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsKCX C 220, POSTRANSLATIONAL MODIFICATION

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.3
Details: 53% SATURATED AMMONIUM SULPHATE, 1.2 M LICL, 20 MM SODIUM CITRATE PH 6.3. SEE ACTA (1998) D54 409-412
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlBPU1drop
220 mMTris-HCl1drop
350 mM1dropNa2SO3
453 %satammonium sulfate1reservoir
51.2 M1reservoirLiCl
620 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8855
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 1996 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8855 Å / Relative weight: 1
ReflectionResolution: 1.65→14 Å / Num. obs: 114679 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 10.22 % / Rmerge(I) obs: 0.076 / Rsym value: 7.6 / Net I/σ(I): 16.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / Rsym value: 59 / % possible all: 97.8
Reflection
*PLUS
Num. obs: 63765 / Num. measured all: 836977

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBP

1ubp


Resolution: 2→20 Å / SU B: 2.04 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1275 2 %RANDOM
Rwork0.16 ---
obs0.16 836977 96.7 %-
Displacement parametersBiso mean: 21.15 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 7 881 6943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7253
X-RAY DIFFRACTIONp_mcangle_it2.1765
X-RAY DIFFRACTIONp_scbond_it3.7016
X-RAY DIFFRACTIONp_scangle_it4.5968
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.67
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.162 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.16 / Num. reflection obs: 63765
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04

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