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- PDB-1i2w: BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 COMPLEXED WITH CEF... -

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Basic information

Entry
Database: PDB / ID: 1i2w
TitleBETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 COMPLEXED WITH CEFOXITIN
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / serine beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / 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. ...Beta-lactamase / 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
Chem-1QL / CARBAMIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFonze, E. / Vanhove, M. / Dive, G. / Sauvage, E. / Frere, J.M. / Charlier, P.
Citation
Journal: Biochemistry / Year: 2002
Title: Crystal structures of the Bacillus licheniformis BS3 class A beta-lactamase and of the acyl-enzyme adduct formed with cefoxitin
Authors: Fonze, E. / Vanhove, M. / Dive, G. / Sauvage, E. / Frere, J.M. / Charlier, P.
#1: Journal: FEBS Lett. / Year: 1997
Title: Unexpected influence of a C-terminal-fused His-tag on the processing of an enzyme and on the kinetic and folding parameters
Authors: Ledent, P. / Duez, C. / Vanhove, M. / Lejeune, A. / Fonze, E. / Charlier, P. / Rhazi-Filali, F. / Thamm, I. / Guillaume, G. / Samyn, B. / Devreese, B. / Van Beeumen, J. / Lamotte-Brasseur, J. / Frere, J.M.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Sep 12, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4925
Polymers62,5722
Non-polymers9203
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.344, 106.372, 63.873
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer

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Components

#1: Protein BETA-LACTAMASE


Mass: 31286.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Plasmid: P-ET-22(B)KR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P00808, beta-lactamase
#2: Chemical ChemComp-1QL / (2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefoxitin, bound form


Mass: 429.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O7S2
#3: Chemical ChemComp-OUT / CARBAMIC ACID


Mass: 61.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 %PEG60001reservoir
3100 mMsodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 1.654→22.029 Å / Num. all: 68766 / Num. obs: 68766 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 5.4
Reflection shellResolution: 1.654→1.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.67 / % possible all: 75.2
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 22.03 Å / Num. measured all: 143995 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.97 Å / % possible obs: 87.1 % / Num. unique obs: 26718 / Num. measured obs: 54861 / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR(ONLINE) 3.851refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALAdata scaling
Agrovatadata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3240 5.1 %RANDOM
Rwork0.216 ---
obs0.216 63397 92.6 %-
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3999 0 52 129 4180
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.761.5
X-RAY DIFFRACTIONx_mcangle_it2.752
X-RAY DIFFRACTIONx_scbond_it3.592
X-RAY DIFFRACTIONx_scangle_it5.822.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.438 307 5.2 %
Rwork0.44 5584 -
obs--86.7 %
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.96
X-RAY DIFFRACTIONx_mcbond_it1.761.5
X-RAY DIFFRACTIONx_scbond_it3.592
X-RAY DIFFRACTIONx_mcangle_it2.752
X-RAY DIFFRACTIONx_scangle_it5.822.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.438 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.44

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