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

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Basic information

Entry
Database: PDB / ID: 1krc
TitleCRYSTAL STRUCTURE OF KLEBSIELLA AEROGENES UREASE, ITS APOENZYME AND TWO ACTIVE SITE MUTANTS
Components(UREASE) x 3
KeywordsHYDROLASE (UREA AMIDO) / ACTIVE SITE 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
CARBON DIOXIDE / 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 / 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)83,2746
Polymers83,1123
Non-polymers1613
Water2,864159
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)249,82218
Polymers249,3379
Non-polymers4849
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48590 Å2
ΔGint-315 kcal/mol
Surface area55630 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

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Protein , 3 types, 3 molecules ABC

#1: Protein UREASE


Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: H(C 320)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 320)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18315, urease
#3: Protein UREASE


Mass: 60299.289 Da / Num. of mol.: 1 / Mutation: H(C 320)A / Source method: isolated from a natural source / Source: (natural) Klebsiella aerogenes (bacteria) / Organ: BEAN / References: UniProt: P18314, urease

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Non-polymers , 3 types, 162 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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsHOH 1, THE CATALYTIC WATER, BRIDGES THE TWO NICKEL IONS. LYS 217 IS COVALENTLY MODIFIED AT NZ BY ...HOH 1, THE CATALYTIC WATER, BRIDGES THE TWO NICKEL IONS. LYS 217 IS COVALENTLY MODIFIED AT NZ BY CO2. NI1 IS COORDINATED BY TWO NITROGENS (HIS 246 AND HIS 272) AND TWO OXYGENS (LYS 217*) LIGANDS IN A PSEUDO-TETRAHEDRAL GEOMETRY. NI2 IS COORDINATED BY TWO NITROGENS (HIS 134 AND HIS 136) AND THREE OXYGENS (ASP 360, HOH 1, LYS 217*) LIGANDS IN A ROUGHLY SQUARE PYRAMIDAL GEOMETRY. 1KAU= 2.2 ANGSTROM STRUCTURE-COMPLETE NICKEL COORDINATION CONTAINS THE FULLY COORDINATED NICKEL METALLOCENTER.

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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 ℃ / Method: vapor diffusion, hanging drop / pH: 7 / 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 MARK II / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→99.9 Å / Num. obs: 28672 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.094
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.094

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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
Details: RESIDUES 308 - 330 IN CHAIN C HAVE HIGH B VALUES. THEY CORRESPOND TO A MOBILE LOOP NEAR THE ACTIVE SITE.
RfactorNum. reflection% reflection
Rwork0.18 --
obs0.18 27755 98 %
Displacement parametersBiso mean: 12.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 5 159 5943
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_deg1.88
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: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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