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- PDB-1s3t: BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1s3t
TitleBORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
Components
  • Urease alpha subunit
  • Urease beta subunit
  • Urease gamma subunit
KeywordsHYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / METALLOENZYME / borate
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
BORIC 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: 2.1 Å
AuthorsBenini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2004
Title: Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism.
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S. / Ciurli, S.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2001
Title: Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism
Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
#2: 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.
#3: 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.
#4: 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. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S.
#5: 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.
History
DepositionJan 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 8, 2015Group: Source and taxonomy
Revision 1.4Aug 23, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.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_ref_seq_dif.details / _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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICALLY FUNCTIONAL MOLECULE IS A TRIMER.
Remark 999SEQUENCE THE AUTHOR STATES THAT THE RESIDUES LISTED IN SEQADV ARE WHAT IS SEEN IN THE DENSITY, AND ...SEQUENCE THE AUTHOR STATES THAT THE RESIDUES LISTED IN SEQADV ARE WHAT IS SEEN IN THE DENSITY, AND IT IS NOT CLEAR WHERE THE DISCREPANCIES ARISE FROM.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urease gamma subunit
B: Urease beta subunit
C: Urease alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1037
Polymers86,8273
Non-polymers2754
Water7,314406
1
A: Urease gamma subunit
B: Urease beta subunit
C: Urease alpha subunit
hetero molecules

A: Urease gamma subunit
B: Urease beta subunit
C: Urease alpha subunit
hetero molecules

A: Urease gamma subunit
B: Urease beta subunit
C: Urease alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,30821
Polymers260,4829
Non-polymers82612
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 area48900 Å2
ΔGint-356 kcal/mol
Surface area58120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.906, 130.906, 189.366
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-857-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Urease gamma subunit / Urea amidohydrolase gamma subunit


Mass: 11204.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Strain: dsm33 / References: UniProt: P41022, urease
#2: Protein Urease beta subunit / Urea amidohydrolase


Mass: 13975.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Strain: dsm33 / References: UniProt: P41021, urease
#3: Protein Urease alpha subunit / Urea amidohydrolase


Mass: 61646.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Strain: dsm33 / References: UniProt: P41020, urease

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Non-polymers , 4 types, 410 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.8 M AMS, 100 mM citric acid, 100 mM boric acid , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 21, 2002 / Details: Bent mirror
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.1→24.8 Å / Num. all: 56339 / Num. obs: 56215 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.16 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 13.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.56 / Num. unique all: 2104 / Rsym value: 0.547 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ubp

2ubp


Resolution: 2.1→24.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.449 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.175 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20455 1141 2 %RANDOM
Rwork0.1775 ---
all0.17805 54834 --
obs0.17805 54834 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.65 Å20 Å2
2--1.31 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 11 406 6376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216068
X-RAY DIFFRACTIONr_bond_other_d0.0140.025576
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.968220
X-RAY DIFFRACTIONr_angle_other_deg1.352312945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815788
X-RAY DIFFRACTIONr_chiral_restr0.0770.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026818
X-RAY DIFFRACTIONr_gen_planes_other0.0230.021139
X-RAY DIFFRACTIONr_nbd_refined0.2080.21218
X-RAY DIFFRACTIONr_nbd_other0.2430.26755
X-RAY DIFFRACTIONr_nbtor_other0.0840.23617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2368
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.2275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.244
X-RAY DIFFRACTIONr_mcbond_it0.4721.53913
X-RAY DIFFRACTIONr_mcangle_it0.89426289
X-RAY DIFFRACTIONr_scbond_it1.52832155
X-RAY DIFFRACTIONr_scangle_it2.5724.51931
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.229 72
Rwork0.199 3962

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