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- PDB-1ef2: CRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE -

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Basic information

Entry
Database: PDB / ID: 1ef2
TitleCRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE
Components
  • UREASE ALPHA SUBUNIT
  • UREASE BETA SUBUNIT
  • UREASE GAMMA SUBUNIT
KeywordsHYDROLASE / alpha-beta barrel / 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
: / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsYamaguchi, K. / Cosper, N.J. / Stalhandske, C. / Scott, R.A. / Pearson, M.A. / Karplus, P.A. / Hausinger, R.P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1999
Title: Characterization of metal-substituted Klebsiella aerogenes urease.
Authors: Yamaguchi, K. / Cosper, N.J. / Stalhandske, C. / Scott, R.A. / Pearson, M.A. / Karplus, P.A. / Hausinger, R.P.
History
DepositionFeb 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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.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_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 ALPHA SUBUNIT
B: UREASE BETA SUBUNIT
C: UREASE GAMMA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6155
Polymers82,5053
Non-polymers1102
Water3,171176
1
A: UREASE ALPHA SUBUNIT
B: UREASE BETA SUBUNIT
C: UREASE GAMMA SUBUNIT
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)247,84415
Polymers247,5149
Non-polymers3306
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48150 Å2
ΔGint-284 kcal/mol
Surface area55260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.8, 170.8, 170.8
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number199
Space group name H-MI213

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Components

#1: Protein UREASE ALPHA SUBUNIT


Mass: 60278.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18314, urease
#2: Protein UREASE BETA SUBUNIT


Mass: 11125.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18315, urease
#3: Protein UREASE GAMMA SUBUNIT


Mass: 11100.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P18316, urease
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate, HEPES, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMHEPES1reservoir
21.6 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 27559 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.322

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
SCALEPACKdata scaling
RefinementResolution: 2.5→10 Å / Rfactor Rwork: 0.172 / σ(F): 0 / Stereochemistry target values: Engh and Huber
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 2 176 5968
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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