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- PDB-1ubp: CRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WIT... -

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Basic information

Entry
Database: PDB / ID: 1ubp
TitleCRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WITH BETA-MERCAPTOETHANOL AT 1.65 ANGSTROMS RESOLUTION
Components(UREASE) x 3
KeywordsHYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / BETA-MERCAPTOETHANOL
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, 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
BETA-MERCAPTOETHANOL / 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: 1.65 Å
AuthorsBenini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
Citation
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.
#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: Soil Biol.Biochem. / Year: 1996
Title: Bacillus Pasteurii Urease: A Heteropolymeric 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
DepositionJan 21, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 30, 2014Group: Database references
Revision 1.4Nov 13, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 1.5Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UREASE
B: UREASE
C: UREASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6547
Polymers86,3813
Non-polymers2744
Water18,2131011
1
A: UREASE
B: UREASE
C: UREASE
hetero molecules

A: UREASE
B: UREASE
C: UREASE
hetero molecules

A: UREASE
B: UREASE
C: UREASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,96321
Polymers259,1429
Non-polymers82112
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 area49440 Å2
ΔGint-296 kcal/mol
Surface area60610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.343, 131.343, 190.013
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 , 3 types, 3 molecules ABC

#1: Protein UREASE / UREA AMINOHYDROLASE


Mass: 11204.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / References: UniProt: P41022, urease
#2: Protein UREASE / 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 / References: UniProt: P41021, urease
#3: Protein UREASE / 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 / References: UniProt: P41020, urease

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Non-polymers , 3 types, 1015 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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1011 / 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: pH 6.30
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlenzyme1drop
220 mMsodium citrate1drop
31
41
51
61
71
81
91

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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: SEGMENTED 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: 0.076 / 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: 0.59 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 14 Å / Observed criterion σ(I): -3 / Num. measured all: 1172081
Reflection shell
*PLUS
% possible obs: 97.8 % / Mean I/σ(I) obs: 2.2

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Processing

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

1kau
PDB Unreleased entry


Resolution: 1.65→14 Å / σ(F): 0
Details: ALL THE ATOMS WITH OCCUPANCY 0 ARE IN DISORDERED REGIONS OR WITHOUT DENSITY.
RfactorNum. reflection% reflection
Rwork0.158 --
obs0.158 114208 98.7 %
Displacement parametersBiso mean: 17.75 Å2
Refinement stepCycle: LAST / Resolution: 1.65→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 10 1011 7077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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