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- PDB-1kgf: STRUCTURE OF BETA-LACTAMASE ASN 170 GLN MUTANT -

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Basic information

Entry
Database: PDB / ID: 1kgf
TitleSTRUCTURE OF BETA-LACTAMASE ASN 170 GLN MUTANT
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / PLASMID / TRANSPOSABLE ELEMENT
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsChen, C.C.H. / Zawadzke, L.E. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 1996
Title: Elimination of the hydrolytic water molecule in a class A beta-lactamase mutant: crystal structure and kinetics.
Authors: Zawadzke, L.E. / Chen, C.C. / Banerjee, S. / Li, Z. / Wasch, S. / Kapadia, G. / Moult, J. / Herzberg, O.
#1: Journal: Biochemistry / Year: 1996
Title: Structure and Kinetics of the Beta-Lactamase Mutants S70A and K73H from Staphylococcus Aureus Pc1
Authors: Chen, C.C. / Smith, T.J. / Kapadia, G. / Wasch, S. / Zawadzke, L.E. / Coulson, A. / Herzberg, O.
#2: Journal: Protein Eng. / Year: 1995
Title: An Engineered Staphylococcus Aureus Pc1 Beta-Lactamase that Hydrolyses Third-Generation Cephalosporins
Authors: Zawadzke, L.E. / Smith, T.J. / Herzberg, O.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0
Authors: Herzberg, O.
#4: Journal: Science / Year: 1987
Title: Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 A Resolution
Authors: Herzberg, O. / Moult, J.
History
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX SECONDARY STRUCTURE ASSIGNMENT IS ACCORDING TO W. KABSCH AND C. SANDER (BIOPOLYMERS 22, 2577- ...HELIX SECONDARY STRUCTURE ASSIGNMENT IS ACCORDING TO W. KABSCH AND C. SANDER (BIOPOLYMERS 22, 2577-2637, 1983). HELIX NUMBERING IS AS IN 3BLM.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)28,9881
Polymers28,9881
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.300, 94.800, 140.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BETA-LACTAMASE / PENICILLINASE


Mass: 28988.434 Da / Num. of mol.: 1 / Mutation: N170Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: PC1 / Description: INDUCIBLE TRC PROMOTER / Gene: BLAZ / Plasmid: PTS32 / Gene (production host): BLAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00807, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING IS BASED ON AMBLER, 1979 (R. P. AMBLER, BETA-LACTAMASES, J. M. T. HAMILTON-MILLER ...RESIDUE NUMBERING IS BASED ON AMBLER, 1979 (R. P. AMBLER, BETA-LACTAMASES, J. M. T. HAMILTON-MILLER AND J. T. SMITH, EDS., ACADEMIC PRESS, NEW YORK, 1979, PP. 99-125), AND ON AMBLER ET AL., BIOCHEM J., V. 276, 269, 1991.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 65 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-6.5 mg/mlenzyme1drop
242 %satammonium sulfate1drop
30.2 %(w/v)PEG20001drop
40.15 M1dropKCl
50.05 M1dropNaHCO3
684 %satammonium sulfate1reservoir
70.4 %(w/v)PEG20001reservoir
80.3 M1reservoirKCl
90.1 M1reservoirNaHCO3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 14, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16464 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 28166
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 76 % / Rmerge(I) obs: 0.215

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.179 -
obs0.179 15046
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 219 2249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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_deg2
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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