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- PDB-2kau: THE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES AT 2.2 ... -

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Basic information

Entry
Database: PDB / ID: 2kau
TitleTHE CRYSTAL STRUCTURE OF UREASE FROM KLEBSIELLA AEROGENES AT 2.2 ANGSTROMS RESOLUTION
Components
  • UREASE (ALPHA CHAIN)
  • UREASE (BETA CHAIN)
  • UREASE (GAMMA CHAIN)
KeywordsHYDROLASE / 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 Å
AuthorsJabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A.
Citation
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.
#1: Journal: Science / Year: 1995
Title: Requirement of Carbon Dioxide for in Vitro Assembly of the Urease Nickel Metallocenter
Authors: Park, I.-S. / Hausinger, R.P.
#2: 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
DepositionFeb 16, 1995Processing site: BNL
Revision 1.0Jul 10, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE ACTIVE SITE AND BI-NICKEL METALLOCENTER ARE LOCATED IN CHAIN C AT THE C-TERMINUS OF THE ...SHEET THE ACTIVE SITE AND BI-NICKEL METALLOCENTER ARE LOCATED IN CHAIN C AT THE C-TERMINUS OF THE STRANDS IN AN ALPHA-BETA BARREL. THIS BARREL IS STRUCTURALLY HOMOLOGOUS TO THAT OF ADENOSINE DEAMINASE, A MONO-ZINC METALLOENZYME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UREASE (GAMMA CHAIN)
B: UREASE (BETA CHAIN)
C: UREASE (ALPHA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3405
Polymers83,2233
Non-polymers1172
Water3,873215
1
A: UREASE (GAMMA CHAIN)
B: UREASE (BETA CHAIN)
C: UREASE (ALPHA CHAIN)
hetero molecules

A: UREASE (GAMMA CHAIN)
B: UREASE (BETA CHAIN)
C: UREASE (ALPHA CHAIN)
hetero molecules

A: UREASE (GAMMA CHAIN)
B: UREASE (BETA CHAIN)
C: UREASE (ALPHA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,02015
Polymers249,6689
Non-polymers3526
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48300 Å2
ΔGint-326 kcal/mol
Surface area55340 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
4: RESIDUE KCX C 217 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. IT COORDINATES NI C 774 THROUGH ITS TERMINAL O ATOMS
DetailsTHREE NONIDENTICAL CHAINS, GAMMA (A), BETA (B), AND ALPHA (C), FORM ONE (ABC)-UNIT. THE ASYMMETRIC UNIT CONTAINS ONE (ABC)-UNIT. THE GAMMA CHAIN WAS CHOSEN AS CHAIN A BECAUSE IT HAS SEQUENCE HOMOLOGY TO THE N-TERMINUS OF THE ONE-SUBUNIT JACK BEAN UREASES, WHEREAS THE K. AEROGENES ALPHA CHAIN C HAS SEQUENCE HOMOLOGY TO THE C-TERMINUS OF JACK BEAN UREASE. THREE UNITS (A, B, C) PACK TIGHTLY AT THE CRYSTALLOGRAPHIC THREE-FOLD TO FORM A TRIMER OF TRIMERS OBSERVED IN SOLUTION. SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. TRIMER 2 OF TRIMER OF TRIMERS APPLIED TO RESIDUES: A 1 .. A 100 SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 1 1.000000 0.000000 0.000000 0.00000 APPLIED TO RESIDUES: B 1 .. B 101 SYMMETRY1 2 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 2 1.000000 0.000000 0.000000 0.00000 APPLIED TO RESIDUES: C 1 .. C 767 SYMMETRY1 3 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 3 0.000000 0.000000 1.000000 0.00000 SYMMETRY3 3 1.000000 0.000000 0.000000 0.00000 TRIMER 3 OF TRIMER OF TRIMERS APPLIED TO RESIDUES: A 1 .. A 100 SYMMETRY1 4 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 4 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 4 0.000000 1.000000 0.000000 0.00000 APPLIED TO RESIDUES: B 1 .. B 101 SYMMETRY1 5 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 5 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 5 0.000000 1.000000 0.000000 0.00000 APPLIED TO RESIDUES: C 1 .. C 767 SYMMETRY1 6 0.000000 0.000000 1.000000 0.00000 SYMMETRY2 6 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 6 0.000000 1.000000 0.000000 0.00000

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Components

#1: Protein UREASE (GAMMA CHAIN)


Mass: 11100.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREC / Organ: BEAN / Plasmid: PKAU19 / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18316, urease
#2: Protein UREASE (BETA CHAIN)


Mass: 11712.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREB / Organ: BEAN / Plasmid: PKAU19 / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18315, urease
#3: Protein UREASE (ALPHA CHAIN)


Mass: 60409.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA / Organ: BEAN / Plasmid: PKAU19 / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / 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.: 215 / 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.
Nonpolymer detailsNI C 774 IS COORDINATED BY ND1 HIS C 246, NE2 HIS C 272, AND O1 LYS C 217 IN A PSEUDO TETRAHEDRAL ...NI C 774 IS COORDINATED BY ND1 HIS C 246, NE2 HIS C 272, AND O1 LYS C 217 IN A PSEUDO TETRAHEDRAL GEOMETRY WITH AN EMPTY FOURTH SITE. NI C 775 IS COORDINATED BY NE2 HIS C 134, NE2 HIS C 136, OD1 ASP C 360, O LYS C 217, AND O HOH 1 IN A ROUGHLY TRIGONAL BIPYRAMIDAL OR SQUARE PYRAMIDAL GEOMETRY.

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMHEPES1reservoir
21.6 M1reservoirLi2SO4

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 58334 / % possible obs: 93 % / Redundancy: 7 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 386731 / Rmerge(I) obs: 0.089

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 0
Details: RESIDUES 308 - 335 IN CHAIN C HAVE HIGH B-FACTORS. THEY CORRESPOND TO A MOBILE LOOP NEAR THE ACTIVE SITE.
RfactorNum. reflection% reflection
Rfree0.225 --
Rwork0.185 --
obs0.185 55572 94.6 %
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5787 0 2 215 6004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.98
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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