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- PDB-1fwe: KLEBSIELLA AEROGENES UREASE, C319A VARIANT WITH ACETOHYDROXAMIC A... -

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Basic information

Entry
Database: PDB / ID: 1fwe
TitleKLEBSIELLA AEROGENES UREASE, C319A VARIANT WITH ACETOHYDROXAMIC ACID (AHA) BOUND
Components(UREASE) x 3
KeywordsHYDROLASE / HYDROLASE(UREA AMIDO) / MUTANT / INHIBITOR-BOUND / 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
ACETOHYDROXAMIC ACID / NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsPearson, M.A. / Karplus, P.A.
Citation
Journal: Biochemistry / Year: 1997
Title: Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease.
Authors: Pearson, M.A. / Michel, L.O. / Hausinger, R.P. / Karplus, P.A.
#1: Journal: Biochemistry / Year: 1996
Title: Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants
Authors: Jabri, E. / Karplus, P.A.
#2: Journal: Science / Year: 1995
Title: The Crystal Structure of Urease from Klebsiella Aerogenes
Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A.
#3: Journal: J.Biol.Chem. / Year: 1992
Title: Site-Directed Mutagenesis of the Active Site Cysteine in Klebsiella Aerogenes Urease
Authors: Martin, P.R. / Hausinger, R.P.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: Identification of the Essential Cysteine Residue in Klebsiella Aerogenes Urease
Authors: Todd, M.J. / Hausinger, R.P.
#5: Journal: J.Biol.Chem. / Year: 1989
Title: Competitive Inhibitors of Klebsiella Aerogenes Urease. Mechanisms of Interaction with the Nickel Active Site
Authors: Todd, M.J. / Hausinger, R.P.
History
DepositionApr 23, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

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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)83,3836
Polymers83,1903
Non-polymers1923
Water4,990277
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)250,14918
Polymers249,5719
Non-polymers5779
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area47190 Å2
ΔGint-302 kcal/mol
Surface area55720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.800, 170.800, 170.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein UREASE / UREA AMIDOHYDROLASE


Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: C(C 319)A
Source method: isolated from a genetically manipulated source
Details: INHIBITOR BOUND / Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU17 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18316, urease
#2: Protein UREASE / UREA AMIDOHYDROLASE


Mass: 11712.239 Da / Num. of mol.: 1 / Mutation: C(C 319)A
Source method: isolated from a genetically manipulated source
Details: INHIBITOR BOUND / Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU17 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18315, urease
#3: Protein UREASE / UREA AMIDOHYDROLASE


Mass: 60377.289 Da / Num. of mol.: 1 / Mutation: C(C 319)A
Source method: isolated from a genetically manipulated source
Details: INHIBITOR BOUND / Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU17 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18314, urease

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Non-polymers , 3 types, 280 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-HAE / ACETOHYDROXAMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHIS MODEL IS THAT OF THE C319A MUTANT WITH THE COMPETITIVE INHIBITOR ACETOHYDROXAMIC ACID (AHA) ...THIS MODEL IS THAT OF THE C319A MUTANT WITH THE COMPETITIVE INHIBITOR ACETOHYDROXAMIC ACID (AHA) BOUND. THREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C) FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT. RESIDUES 318 - 331 OF THE MOBILE ACTIVE SITE FLAP IN CHAIN C BECOME SUFFICIENTLY DISORDERED THAT THEY ARE NOT MODELED. THE AHA MOLECULE INTERACTS WITH BOTH NICKELS IN THE ACTIVE SITE, AS WELL AS ACCEPTING A HYDROGEN BOND FROM HIS 219, A RESIDUE IMPLICATED IN SUBSTRATE-BINDING.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Jabri, E., (1992) J.Mol.Biol., 227, 934.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlurease1drop
210 mMTris1drop
30.5 mMEDTA1drop
40.5 mMbeta-mercaptoethanol1drop
50.75-0.85 M1dropLi2SO4
650 mMHEPES1drop
71.5-1.7 M1reservoirLi2SO4
8100 mMHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 52075 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 67 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.395

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.204 --
obs0.204 50863 92 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5683 0 7 277 5967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.514
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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