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- PDB-1i2s: BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 -

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Basic information

Entry
Database: PDB / ID: 1i2s
TitleBETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3
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
CITRIC 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,0026
Polymers62,5722
Non-polymers4304
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.362, 106.817, 63.901
Angle α, β, γ (deg.)90.00, 94.43, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.22 %
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: AREA DETECTOR / 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: 1.653→23.74 Å / Num. all: 70471 / Num. obs: 70471 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 5.4
Reflection shellResolution: 1.653→1.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.9 / % possible all: 79.1
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 23.74 Å / Num. measured all: 165623
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.97 Å / % possible obs: 89.7 % / Num. possible: 27770 / Num. measured obs: 64168 / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9

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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: 0.004 / 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
Rfree0.237 3316 5.1 %RANDOM
Rwork0.197 ---
obs0.197 64762 94.1 %-
all-65093 --
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 28 152 4170
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.69
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.551.5
X-RAY DIFFRACTIONx_mcangle_it2.512
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_scangle_it5.682.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.362 315 5.1 %
Rwork0.351 5866 -
obs--90.2 %
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 / Rfactor Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.69
X-RAY DIFFRACTIONx_mcbond_it1.551.5
X-RAY DIFFRACTIONx_scbond_it3.42
X-RAY DIFFRACTIONx_mcangle_it2.512
X-RAY DIFFRACTIONx_scangle_it5.682.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.351

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