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- PDB-1ome: CRYSTAL STRUCTURE OF THE OMEGA LOOP DELETION MUTANT (RESIDUES 163... -

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Basic information

Entry
Database: PDB / ID: 1ome
TitleCRYSTAL STRUCTURE OF THE OMEGA LOOP DELETION MUTANT (RESIDUES 163-178 DELETED) OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / BETA-LACTAM ANTIBIOTIC RESISTANCE
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBanerjee, S. / Pieper, U. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 1998
Title: Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase.
Authors: Banerjee, S. / Pieper, U. / Kapadia, G. / Pannell, L.K. / 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 A Resolution
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
DepositionFeb 9, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9843
Polymers57,9492
Non-polymers351
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.000, 55.000, 79.200
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-LACTAMASE / PENICILLINASE


Mass: 28974.406 Da / Num. of mol.: 2 / Mutation: DELETION OF AN OMEGA LOOP (RESIDUES 163 - 178)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: PC1
Description: INDUCIBLE TRC PROMOTOR PKK233-2 DERIVATIVE WITH TN9 CAT GENE INSERTED INTO TEM BLAZ
Gene: BLAZ / Plasmid: PTS32 / Gene (production host): BLAZ / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00807, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING SCHEME IS ACCORDING TO AMBLER ET AL., BIOCHEM. J. 276:269-272, 1991.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 58 %
Crystal growpH: 8
Details: 68% SATURATED AMMONIUM SULFATE, 0.5% PEG 1000, 0.3M KCL, 0.1M SODIUM BICARBONATE PH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.0 mg/mlenzyme1drop
234 %satammonium sulfate1drop
30.25 %PEG10001drop
40.15 Mpotassium chloride1drop
50.05 Msodium bicarbonate1drop
668 %satammonium sulfate1reservoir
70.5 %PEG10001reservoir
80.3 Mpotassium chloride1reservoir
90.1 Msodium bicarbonate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: SIEMENS MIRRORS
RadiationMonochromator: SIEMENS MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 25484 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 70
Reflection
*PLUS
Num. all: 29398
Reflection shell
*PLUS
% possible obs: 70 % / Num. measured obs: 4822

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BLM

3blm


Resolution: 2.3→7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 2288 10 %RANDOM
Rwork0.19 ---
obs0.19 23262 79 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 1 181 3926
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_deg3.4
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_d1.4
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: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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