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- PDB-4ubp: STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROX... -

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Basic information

Entry
Database: PDB / ID: 4ubp
TitleSTRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION
Components(PROTEIN (UREASE (CHAIN ...) x 3
KeywordsHYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / ACETOHYDROXAMIC ACID / 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
ACETOHYDROXAMIC ACID / 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: 1.55 Å
AuthorsBenini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2000
Title: The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Miletti, S. / Ciurli, S. / Mangani, S.
#1: Journal: Structure / 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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
DepositionFeb 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Assembly

Deposited unit
A: PROTEIN (UREASE (CHAIN A))
B: PROTEIN (UREASE (CHAIN B))
C: PROTEIN (UREASE (CHAIN C))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0026
Polymers86,8093
Non-polymers1923
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-50 kcal/mol
Surface area30140 Å2
MethodPISA
2
A: PROTEIN (UREASE (CHAIN A))
B: PROTEIN (UREASE (CHAIN B))
C: PROTEIN (UREASE (CHAIN C))
hetero molecules

A: PROTEIN (UREASE (CHAIN A))
B: PROTEIN (UREASE (CHAIN B))
C: PROTEIN (UREASE (CHAIN C))
hetero molecules

A: PROTEIN (UREASE (CHAIN A))
B: PROTEIN (UREASE (CHAIN B))
C: PROTEIN (UREASE (CHAIN C))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,00518
Polymers260,4289
Non-polymers5779
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 area48810 Å2
ΔGint-286 kcal/mol
Surface area60130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.880, 130.880, 189.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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

#1: Protein PROTEIN (UREASE (CHAIN A)) / 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 (CHAIN B)) / 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 (CHAIN C)) / 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, 749 molecules

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


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-HAE / ACETOHYDROXAMIC ACID / Acetohydroxamic acid


Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: inhibitor, medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 746 / 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 growpH: 6.3
Details: ATED AMMONIUM SULPHATE, 1.2 M LICL), DROXAMIC ACID, 1OOMM SODIUM CITRATE PH 6.3. HANGING DROP 20 C, 3 UL PROTEIN SOLUTION (11 MG/ML IN 20 MM TRIS HCL PH 8.0 + 4MM ACETOHYDROXAMIC ACID) + 3 ...Details: ATED AMMONIUM SULPHATE, 1.2 M LICL), DROXAMIC ACID, 1OOMM SODIUM CITRATE PH 6.3. HANGING DROP 20 C, 3 UL PROTEIN SOLUTION (11 MG/ML IN 20 MM TRIS HCL PH 8.0 + 4MM ACETOHYDROXAMIC ACID) + 3 MICROLITERS PRECIPITANT SOLUTION, pH 6.30
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlurease1drop
250 mMsodium phosphate1drop
350 mM1dropNa2SO3
420 mMTris-HCl1drop
54 mMAHA1drop
61.2 M1reservoirLiCl
7100 mMsodium citrate1reservoir
84 mMAHA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8342
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 1998 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8342 Å / Relative weight: 1
ReflectionResolution: 1.55→35 Å / Num. obs: 138830 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 26.02 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 15.03
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.23 / Rsym value: 0.479 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 32.5 Å / % possible obs: 99.5 % / Num. measured all: 3612270
Reflection shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.58 Å / % possible obs: 99.5 % / Mean I/σ(I) obs: 2.2

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Processing

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

2ubp


Resolution: 1.55→32.73 Å / Cross valid method: RFREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2754 2 %RANDOM
Rwork0.1513 ---
obs0.1513 136971 99.5 %-
Displacement parametersBiso mean: 26.22 Å2
Refinement stepCycle: LAST / Resolution: 1.55→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 7 746 6809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2512
X-RAY DIFFRACTIONp_mcangle_it2.9573
X-RAY DIFFRACTIONp_scbond_it2.9772
X-RAY DIFFRACTIONp_scangle_it3.9843
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor13.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151 / Rfactor Rwork: 0.151 / Highest resolution: 1.55 Å / Lowest resolution: 32.7 Å / Rfactor Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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