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- PDB-1tem: 6 ALPHA HYDROXYMETHYL PENICILLOIC ACID ACYLATED ON THE TEM-1 BETA... -

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Basic information

Entry
Database: PDB / ID: 1tem
Title6 ALPHA HYDROXYMETHYL PENICILLOIC ACID ACYLATED ON THE TEM-1 BETA-LACTAMASE FROM ESCHERICHIA COLI
ComponentsTEM-1 BETA LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / TRANSPOSABLE ELEMENT
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-ALP / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsMaveyraud, L. / Massova, I. / Samama, J.P. / Mobashery, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 1996
Title: Crystal Structure of 6Alpha-Hydroxymethylpenicillanate Complexed to the Tem-1 Beta-Lactamase from Escherichia Coli: Evidence on the Mechanism of Action of a Novel Inhibitor Designed by a Computer-Aided Process
Authors: Maveyraud, L. / Massova, I. / Birck, C. / Miyashita, K. / Samama, J.P. / Mobashery, S.
#1: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Design, Synthesis, and Evaluation of a Potent Mechanism-Based Inhibitor for the Tem Beta-Lactamase with Implications for the Enzyme Mechanism
Authors: Miyashita, K. / Massova, I. / Taibi, P. / Mobashery, S.
History
DepositionMay 28, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification / _software.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_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: TEM-1 BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2332
Polymers28,9841
Non-polymers2491
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.100, 63.100, 88.800
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 TEM-1 BETA LACTAMASE


Mass: 28984.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VARIANT V84I, A184V,ACYL-ENZYME COMPLEX / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-ALP / 2-(1-CARBOXY-2-HYDROXY-ETHYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID


Mass: 249.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX, BETWEEN 6ALPHA-HYDROXYMETHYL PENICILLOIC ACID ...THE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX, BETWEEN 6ALPHA-HYDROXYMETHYL PENICILLOIC ACID AND THE TEM 1 BETA-LACTAMASE FROM ESCHERICHIA COLI. THE ACYLATED RESIDUE IS SER 70.
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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, hanging drop / Details: Jelsch, C., (1992) J. Mol. Biol., 223, 377.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
260 mMsodium phosphate1drop
310 %satammonium sulfate1drop
460 mMsodium phosphate1reservoir
546 %satammonium sulfate1reservoir
64 %aceton1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionNum. obs: 17104 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 12.49 Å2 / Rmerge(I) obs: 0.046
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 22 Å / Num. measured all: 42284
Reflection shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2.02 Å / % possible obs: 94.8 % / Num. unique obs: 1524 / Num. measured obs: 3622 / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
Agrovatadata collection
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementResolution: 1.95→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.202 -10 %
Rwork0.156 --
obs0.156 16853 -
Displacement parametersBiso mean: 12.35 Å2
Refine analyzeLuzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 15 234 2286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.269
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
LS refinement shellResolution: 1.95→1.98 Å
RfactorNum. reflection% reflection
Rfree0.242 -10 %
Rwork0.183 636 -
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.359 Å2

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