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- PDB-1ie7: PHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1ie7
TitlePHOSPHATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE
Components
  • UREASE ALPHA SUBUNIT
  • UREASE BETA SUBUNIT
  • UREASE GAMMA SUBUNIT
KeywordsHYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / 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, 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 / PHOSPHATE ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBenini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S.
Citation
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.
#1: 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.
#2: 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.
#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. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S.
#4: 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
DepositionApr 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 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.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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE There are differences between the original sequence from DNA reported by others and the ...SEQUENCE There are differences between the original sequence from DNA reported by others and the electron density maps, including an insertion. The modified residues are due to posttranslational modifications.

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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)87,0266
Polymers86,8133
Non-polymers2123
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-59 kcal/mol
Surface area30210 Å2
MethodPISA
2
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)261,07718
Polymers260,4409
Non-polymers6379
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 area48260 Å2
ΔGint-309 kcal/mol
Surface area60720 Å2
MethodPISA
3
A: UREASE GAMMA SUBUNIT

B: UREASE BETA SUBUNIT
C: UREASE ALPHA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0266
Polymers86,8133
Non-polymers2123
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_565-x+y,-x+1,z1
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-60 kcal/mol
Surface area29390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.489, 131.489, 189.489
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 GAMMA SUBUNIT / UREA AMIDOHYDROLASE


Mass: 11204.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Strain: DSM 33 / 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: DSM 33 / References: UniProt: P41021, urease
#3: Protein UREASE ALPHA SUBUNIT / UREA AMIDOHYDROLASE


Mass: 61632.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Strain: DSM 33 / References: UniProt: P41020, urease

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Non-polymers , 3 types, 899 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / 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: 2.99 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.8 M AMS, 100 mM Sodium Phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 K / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop
250 mMsodium phosphate1droppH7.5
350 mM1dropNa2SO3
41.6-1.8 Mammonium sulfate1reservoir
5100 mMsodium phosphate1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.834 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 1998 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 1.85→11.987 Å / Num. all: 82718 / Num. obs: 379334 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.58 % / Biso Wilson estimate: 22.08 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.85 / Num. unique all: 3824 / Rsym value: 0.448 / % possible all: 94.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 82718 / Redundancy: 4.61 % / Num. measured all: 381291
Reflection shell
*PLUS
% possible obs: 94.3 % / Redundancy: 3.2 %

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Processing

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

2ubp


Resolution: 1.85→11.99 Å / SU B: 2.8591 / SU ML: 0.0826 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.1183 / ESU R Free: 0.1161 / Stereochemistry target values: Engh & Huber
Details: THE PROTEIN ATOMS INVOLVED IN CLOSE CONTACTS WITH WATERS IN REMARK 500 ARE DISORDERED AS INDICATED BY THEIR OCCUPANCY = 0. The residue ASN C 327 that has a chirality error at the CA center ...Details: THE PROTEIN ATOMS INVOLVED IN CLOSE CONTACTS WITH WATERS IN REMARK 500 ARE DISORDERED AS INDICATED BY THEIR OCCUPANCY = 0. The residue ASN C 327 that has a chirality error at the CA center is located in a very disordered region in the electron desity map.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1607 2 %RANDOM
Rwork0.17 ---
obs0.19 80351 99.3 %-
all-80351 --
Displacement parametersBiso mean: 30.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 7 896 6957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_planar_d0.440.5
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor14.515
X-RAY DIFFRACTIONp_transverse_tor29.120
X-RAY DIFFRACTIONp_mcbond_it1.8913
X-RAY DIFFRACTIONp_mcangle_it2.3745
X-RAY DIFFRACTIONp_scbond_it3.9436
X-RAY DIFFRACTIONp_scangle_it5.038
X-RAY DIFFRACTIONp_special_tor015
LS refinement shellResolution: 1.85→1.93 Å
RfactorNum. reflection% reflection
Rfree0.316 204 -
Rwork0.3 --
obs-9374 94.3 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 2 % / Rfactor obs: 0.173 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_planar_d0.440.5
X-RAY DIFFRACTIONp_plane_restr0.067
X-RAY DIFFRACTIONp_mcbond_it3
X-RAY DIFFRACTIONp_scbond_it6
X-RAY DIFFRACTIONp_mcangle_it5
X-RAY DIFFRACTIONp_scangle_it8

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