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- PDB-1krb: CRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME A... -

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Basic information

Entry
Database: PDB / ID: 1krb
TitleCRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS
Components(UREASE) x 3
KeywordsHYDROLASE / ACTIVE SITE MUTANT / NICKEL METALLOENZYME / HYDROLASE (UREA AMIDO)
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: 2.5 Å
AuthorsJabri, E. / Karplus, P.A.
Citation
Journal: Biochemistry / Year: 1996
Title: Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants.
Authors: Jabri, E. / Karplus, P.A.
#1: 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.
#2: 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.-L. / Hausinger, R.P.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Preliminary Crystallographic Studies of Urease from Jack Bean and from Klebsiella Aerogenes
Authors: Jabri, E. / Lee, M.H. / Hausinger, R.P. / Karplus, P.A.
History
DepositionJun 20, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)83,2735
Polymers83,1553
Non-polymers1172
Water2,738152
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)249,81915
Polymers249,4669
Non-polymers3526
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48170 Å2
ΔGint-318 kcal/mol
Surface area55140 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
Atom site foot note1: CIS PROLINE - PRO C 282 / 2: CIS PROLINE - PRO C 303 / 3: CIS PROLINE - PRO C 470
DetailsTHREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C) FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT.

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Components

#1: Protein UREASE


Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: H(C 219)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18316, urease
#2: Protein UREASE


Mass: 11712.239 Da / Num. of mol.: 1 / Mutation: H(C 219)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18315, urease
#3: Protein UREASE


Mass: 60342.289 Da / Num. of mol.: 1 / Mutation: H(C 219)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / 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.: 152 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. THIS MODEL IS ...RESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. THIS MODEL IS THAT OF THE H219A MUTANT AT 2.5 ANGSTROMS. THE ACTIVE SITE IS NEARLY IDENTICAL TO THAT OF THE HOLOENZYME (ENTRY 1KAU).

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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: 2.5 Å3/Da / Density % sol: 50.73 %
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
1100 mMHEPES1reservoir
21.6 M1reservoirLi2SO4
3100 mMHEPES1drop
41.6 M1dropLi2SO4
510 mg/mlurease1drop
620 mMTris1drop
71 mMEDTA1drop
81 mMbeta-mercaptoethanol1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99.9 Å / Num. obs: 27404 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.095
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.179 --
obs0.179 26626 98 %
Displacement parametersBiso mean: 10.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5782 0 2 152 5936
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_deg1.91
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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