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- PDB-1fwi: KLEBSIELLA AEROGENES UREASE, H134A VARIANT -

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Basic information

Entry
Database: PDB / ID: 1fwi
TitleKLEBSIELLA AEROGENES UREASE, H134A VARIANT
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, beta subunit ...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: J.Biol.Chem. / Year: 1996
Title: Characterization of the mononickel metallocenter in H134A mutant urease.
Authors: Park, I.S. / Michel, L.O. / Pearson, M.A. / Jabri, E. / Karplus, P.A. / Wang, S. / Dong, J. / Scott, R.A. / Koehler, B.P. / Johnson, M.K. / Hausinger, R.P.
#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: Protein Sci. / Year: 1993
Title: Site-Directed Mutagenesis of Klebsiella Aerogenes Urease: Identification of Histidine Residues that Appear to Function in Nickel Ligation, Substrate Binding, and Catalysis
Authors: Park, I.S. / 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.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)83,2144
Polymers83,1553
Non-polymers591
Water5,549308
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)249,64212
Polymers249,4669
Non-polymers1763
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area45940 Å2
ΔGint-269 kcal/mol
Surface area55430 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: H(C 134)A
Source method: isolated from a genetically manipulated source
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: H(C 134)A
Source method: isolated from a genetically manipulated source
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: 60342.289 Da / Num. of mol.: 1 / Mutation: H(C 134)A
Source method: isolated from a genetically manipulated source
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 / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS MODEL IS THAT OF THE H134A MUTANT AT 2.0 ANGSTROMS. THREE NONIDENTICAL CHAINS, GAMMA (A), BETA ...THIS MODEL IS THAT OF THE H134A MUTANT AT 2.0 ANGSTROMS. THREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C) FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT. RESIDUES 317 - 331 OF THE MOBILE ACTIVE SITE FLAP IN CHAIN C ARE SUFFICIENTLY DISORDERED THAT THEY WERE NOT MODELED NI2 IS NOT PRESENT DUE TO THE LOSS OF THE NICKEL LIGAND HIS 134. NI1 IS NOW LIGATED BY THREE WATER MOLECULES (WATERS 176, 177, AND 179) WHICH ALONG WITH THREE PROTEIN LIGANDS FORM AN OCTAHEDRAL COORDINATION GEOMETRY FOR NI1.

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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: 52421 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 2 Å

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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
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 51455 93 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 1 308 5979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.63
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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