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- PDB-1bt5: CRYSTAL STRUCTURE OF THE IMIPENEM INHIBITED TEM-1 BETA-LACTAMASE ... -

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Basic information

Entry
Database: PDB / ID: 1bt5
TitleCRYSTAL STRUCTURE OF THE IMIPENEM INHIBITED TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI
ComponentsPROTEIN (BETA-LACTAMASE)
KeywordsHYDROLASE / BETA-LACTAM DEGRADATION
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IM2 / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsMaveyraud, L. / Mourey, L. / Pedelacq, J.D. / Guillet, V. / Kotra, L.K. / Mobashery, S. / Samama, J.P.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Structural Basis for Clinical Longevity of Carbapenem Antibiotics in the Face of Challenge by the Common Class A Beta-Lactamases from Antibiotic-Resistant Bacteria
Authors: Maveyraud, L. / Mourey, L. / Kotra, L.P. / Pedelacq, J.D. / Guillet, V. / Mobashery, S. / Samama, J.P.
#1: Journal: Proteins / Year: 1993
Title: Crystal Structure of Escherichia Coli Tem1 Beta-Lactamase at 1.8 A Resolution
Authors: Jelsch, C. / Mourey, L. / Masson, J.M. / Samama, J.P.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Crystallographic Data on Escherichia Coli Tem1 Beta-Lactamase
Authors: Jelsch, C. / Lenfant, F. / Masson, J.M. / Samama, J.P.
History
DepositionSep 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Other
Revision 1.4Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / diffrn_source / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,05410
Polymers28,9841
Non-polymers1,0709
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.420, 62.010, 89.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (BETA-LACTAMASE)


Mass: 28984.076 Da / Num. of mol.: 1 / Mutation: V82I, A182V
Source method: isolated from a genetically manipulated source
Details: ESTER LINK BETWEEN SER A 70 OG AND IM2 350 C7 / Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASMIC / Gene: BLA / Variant: V82I, A182V / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 1.94 Å3/Da / Density % sol: 36.2 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: other / Details: Jelsch, C., (1992) J. Mol. Biol., 223, 377.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1271
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.8→18 Å / Num. obs: 21770 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 12.13 Å2 / Rsym value: 0.059 / Net I/σ(I): 20.9
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.7 / Rsym value: 0.116 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 84646 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.8→18 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: EXTERNAL BULK SOLVENT CORRECTION COMPUTED WITH XPLOR 3.1
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1113 5 %RANDOM
Rwork0.173 ---
obs-21708 98.3 %-
Displacement parametersBiso mean: 10.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 60 347 2437
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0220.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0750.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.531.5
X-RAY DIFFRACTIONp_mcangle_it0.6771
X-RAY DIFFRACTIONp_scbond_it1.2811.5
X-RAY DIFFRACTIONp_scangle_it2.0163
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2670.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor10.92
X-RAY DIFFRACTIONp_staggered_tor16.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.4
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.6
X-RAY DIFFRACTIONp_plane_restr0.0130.02

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