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- PDB-3ubp: DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE -

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Basic information

Entry
Database: PDB / ID: 3ubp
TitleDIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE
Components(PROTEIN (UREASE ...) x 3
KeywordsHYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / DIAMIDOPHOSPHATE / METALLOENZYME
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
DIAMIDOPHOSPHATE / 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. / Miletti, S. / Mangani, S. / Ciurli, 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 1.65A 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
DepositionDec 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 17, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0May 31, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / diffrn_source / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact
Revision 2.2Nov 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)87,0236
Polymers86,8093
Non-polymers2133
Water15,151841
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-52 kcal/mol
Surface area29930 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)261,06818
Polymers260,4289
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 area49990 Å2
ΔGint-291 kcal/mol
Surface area58100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.532, 131.532, 188.451
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
11A-150-

HOH

21A-155-

HOH

31C-1135-

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: 13975.539 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, 844 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-2PA / DIAMIDOPHOSPHATE


Mass: 96.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5N2O2P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.3
Details: WELL SOLUTIONS: 1.9 M AMMONIUM SULPHATE, 4MM PHENYLPHOSPHORODIAMIDATE, 1OOMM SODIUM CITRATE PH 6.3. PROTEIN SOLUTION: 20 C, 3 MICROLITERS PROTEIN SOLUTION ( 11 MG/ML IN 20 MM TRIS HCL PH 8.0 ...Details: WELL SOLUTIONS: 1.9 M AMMONIUM SULPHATE, 4MM PHENYLPHOSPHORODIAMIDATE, 1OOMM SODIUM CITRATE PH 6.3. PROTEIN SOLUTION: 20 C, 3 MICROLITERS PROTEIN SOLUTION ( 11 MG/ML IN 20 MM TRIS HCL PH 8.0 + 4MM PHENYLPHOSPHORODIAMIDATE) + 3 MICROLITERS PRECIPITANT SOLUTION, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
220 mMTris-HCl1drop
34 mMPPD1drop
4100 mMsodium citrate1reservoir
51.9 Mammonium sulfate1reservoir
64 mMPPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 24, 1997 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9995 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 65301 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.38 % / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 9.72
Reflection shellResolution: 2→2.04 Å / Redundancy: 7.56 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.536 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 874166
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UBP

2ubp


Resolution: 2→18 Å / Cross valid method: RFREE / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1306 2 %RANDOM
Rwork0.158 ---
obs0.158 65301 99.9 %-
Displacement parametersBiso mean: 15.87 Å2
Refinement stepCycle: LAST / Resolution: 2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 7 841 6903
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
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_it1.6483
X-RAY DIFFRACTIONp_mcangle_it2.0775
X-RAY DIFFRACTIONp_scbond_it3.8556
X-RAY DIFFRACTIONp_scangle_it4.6348
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.97
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.520
X-RAY DIFFRACTIONp_special_tor015

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