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- PDB-1kgg: STRUCTURE OF BETA-LACTAMASE GLU166GLN:ASN170ASP MUTANT -

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Basic information

Entry
Database: PDB / ID: 1kgg
TitleSTRUCTURE OF BETA-LACTAMASE GLU166GLN:ASN170ASP MUTANT
ComponentsPROTEIN (BETA-LACTAMASE)
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / BETA-LACTAM HYDROLYSIS
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 / OTHER / Resolution: 2.3 Å
AuthorsChen, C.C.H. / Herzberg, O.
Citation
Journal: Protein Eng. / Year: 1999
Title: Relocation of the catalytic carboxylate group in class A beta-lactamase: the structure and function of the mutant enzyme Glu166-->Gln:Asn170-->Asp.
Authors: Chen, C.C. / Herzberg, O.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus PC1 at 2.0
Authors: Herzberg, O.
#3: 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
DepositionMay 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.6Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: PROTEIN (BETA-LACTAMASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0702
Polymers28,9741
Non-polymers961
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.000, 94.800, 138.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

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Components

#1: Protein PROTEIN (BETA-LACTAMASE) / PENICILLINASE


Mass: 28974.410 Da / Num. of mol.: 1 / Mutation: E166Q,N170D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: PC1 / Gene: BLAZ / Plasmid: PTS32 / Gene (production host): BLAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00807, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 65 %
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
189 %satammonium sulfate1reservoir
20.5 %PEG20001reservoir
30.1 Msodium bicarbonate1reservoir
410 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 15531 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.8 / % possible all: 87.1
Reflection shell
*PLUS
% possible obs: 87.1 % / Num. unique obs: 2665

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Processing

Software
NameVersionClassification
X-PLOR3.7refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: OTHER
Starting model: 3BLM

3blm


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1257 10 %RANDOM
Rwork0.178 ---
obs-12688 82 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 5 67 2101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg1.9
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: 3.7 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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