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- PDB-1fwb: KLEBSIELLA AEROGENES UREASE, C319A VARIANT AT PH 6.5 -

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Basic information

Entry
Database: PDB / ID: 1fwb
TitleKLEBSIELLA AEROGENES UREASE, C319A VARIANT AT PH 6.5
Components(UREASE) x 3
KeywordsHYDROLASE / HYDROLASE(UREA AMIDO) / MUTANT / 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 / 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.
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 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_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

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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)83,3085
Polymers83,1903
Non-polymers1172
Water5,062281
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)249,92415
Polymers249,5719
Non-polymers3526
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48290 Å2
ΔGint-321 kcal/mol
Surface area55210 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

#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: PH 6.5 / 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: PH 6.5 / 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: PH 6.5 / Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU17 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18314, urease
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS MODEL IS THAT OF THE C319A MUTANT (PH=6.5) AT 2.0 ANGSTROMS. THE ACTIVE SITE IS NEARLY ...THIS MODEL IS THAT OF THE C319A MUTANT (PH=6.5) AT 2.0 ANGSTROMS. THE ACTIVE SITE IS NEARLY IDENTICAL TO THAT OF THE HOLOENZYME (PDB ENTRY 1KAU). THREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C) FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT. RESIDUES 312 - 336 IN CHAIN C, THE MOBILE ACTIVE SITE FLAP, ARE MORE WELL ORDERED THAN IN THE HOLOENZYME (1KAU). THREE WATERS, 500, 501, AND 502 ARE LIGATED TO THE ACTIVE SITE NICKEL IONS. THEY MUST BE PARTIALLY OCCUPIED DUE TO CLOSE OXYGEN-OXYGEN DISTANCES BETWEEN THEM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 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 MARK II / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 52554 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 70 % / Redundancy: 2 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→10 Å / σ(F): 0
Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE ACTIVE SITE NICKEL IONS AND NICKEL-BOUND WATERS 500, 501, 502. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH ...Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE ACTIVE SITE NICKEL IONS AND NICKEL-BOUND WATERS 500, 501, 502. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH A FIXED B-FACTOR OF 20 ANGSTROMS**2. THE REFINED OCCUPANCIES FOR THESE WATERS SUGGEST NEARLY FULL OCCUPANCY FOR EACH OF THEM, ALTHOUGH THEY ARE POSITIONED TOO CLOSE (~ 2.0 ANGSTROMS APART) FOR SIMULTANEOUS OCCUPANCY. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH A FIXED B-FACTOR OF 20 ANGSTROMS**2. THE REFINED OCCUPANCIES FOR THESE WATERS SUGGEST NEARLY FULL OCCUPANCY FOR EACH OF THEM, ALTHOUGH THEY ARE POSITIONED TOO CLOSE (~ 2.0 ANGSTROMS APART) FOR SIMULTANEOUS OCCUPANCY.
RfactorNum. reflection% reflection
Rwork0.169 --
obs0.169 51930 94 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 2 281 6071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.44
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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