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- PDB-1a5n: K217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED ... -

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Basic information

Entry
Database: PDB / ID: 1a5n
TitleK217A VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL
Components
  • UREASE (ALPHA SUBUNIT)
  • UREASE (BETA SUBUNIT)
  • UREASE (GAMMA SUBUNIT)
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
FORMIC ACID / NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsPearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P.
Citation
Journal: Biochemistry / Year: 1998
Title: Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand.
Authors: Pearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P.
#1: Journal: Acc.Chem.Res. / Year: 1997
Title: 70 Years of Crystalline Urease: What Have We Learned?
Authors: Karplus, P.A. / Pearson, M.A. / Hausinger, R.P.
#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.
History
DepositionFeb 17, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: 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.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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)82,5676
Polymers82,4043
Non-polymers1633
Water3,153175
1
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)247,70118
Polymers247,2119
Non-polymers4909
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area46770 Å2
ΔGint-307 kcal/mol
Surface area55780 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 (GAMMA SUBUNIT)


Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: K217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18316, 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) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18315, urease
#3: Protein UREASE (ALPHA SUBUNIT)


Mass: 60177.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18314, urease

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Non-polymers , 3 types, 178 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.52 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM HEPES, PH 7.5, 1.6 M LI2SO4; THEN CRYSTAL WAS SOAKED IN 100 MM HEPES, 500MM FORMATE, PH 7.2, 2.0 M LI2SO4, 1.5 MM NICL2
PH range: 7.2-7.5
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlurease1drop
210 mMTris-HCl1drop
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

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 31434 / % possible obs: 100 % / Redundancy: 4 % / Rsym value: 0.099 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.333 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.333

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.4→10 Å / σ(F): 0
Details: ALL NON-BONDED INTERACTIONS INVOLVING THE NICKEL IONS OR FORMATE ION WERE REMOVED DURING REFINEMENT. THE OCCUPANCIES FOR THE NICKEL IONS WERE REFINED WITH A FIXED B-FACTOR OF 17 (ANGSTROMS)**2.
RfactorNum. reflection% reflection
Rwork0.167 --
obs0.167 30925 97 %
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 5 175 5846
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_deg1.428
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.263
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
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.226 3839 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNI.PROTOPNI.PRO
X-RAY DIFFRACTION3PARAM-FORM.INPTOP-FORM.INP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.263
LS refinement shell
*PLUS
Rfactor obs: 0.226

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