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- PDB-1erm: X-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A... -

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Basic information

Entry
Database: PDB / ID: 1erm
TitleX-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-1-ACETAMIDO-2-(3-CARBOXYPHENYL)ETHANE BORONIC ACID
ComponentsTEM-1 BETA-LACTAMASE
KeywordsHYDROLASE / beta-lactamase / structure-based design / boronate inhibitor
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-BJI / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsNess, S. / Martin, R. / Kindler, A.M. / Paetzel, M. / Gold, M. / Jones, J.B. / Strynadka, N.C.J.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase(,).
Authors: Ness, S. / Martin, R. / Kindler, A.M. / Paetzel, M. / Gold, M. / Jensen, S.E. / Jones, J.B. / Strynadka, N.C.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Structure-based design of a potent transition state analogue for TEM-1 beta-lactamase
Authors: Strynadka, N.C.J. / Martin, R. / Jensen, S.E. / Gold, M. / Jones, J.B.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2012Group: Non-polymer description
Revision 1.4Nov 13, 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_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_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: TEM-1 BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2092
Polymers28,9581
Non-polymers2511
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.03, 89.06, 42.16
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: 28957.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-BJI / 1(R)-1-ACETAMIDO-2-(3-CARBOXYPHENYL)ETHYL BORONIC ACID


Mass: 251.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14BNO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 1.5 M / Common name: phosphate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 93628 / Num. obs: 93628 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.139 / Num. unique all: 2828 / % possible all: 88
Reflection
*PLUS

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
MLPHAREphasing
TNTrefinement
SDMSdata scaling
RefinementResolution: 1.7→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: bond length = 0.8 bond angle = 0.8 Try plane = 1.0 Gen. plane 1.0 bad contacts = 12 Temp. = 3
RfactorNum. reflection% reflection
Rwork0.177 --
all0.177 22036 -
obs0.177 22036 82 %
Rfree-0 -
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 18 137 2183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONAngle distances0.021
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.9

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