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

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Basic information

Entry
Database: PDB / ID: 1ero
TitleX-RAY CRYSTAL STRUCTURE OF TEM-1 BETA LACTAMASE IN COMPLEX WITH A DESIGNED BORONIC ACID INHIBITOR (1R)-2-PHENYLACETAMIDO-2-(3-CARBOXYPHENYL)ETHYL 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 / beta-lactamase activity / 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-BJP / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsNess, S. / Martin, R. / Kindler, A.M. / Paetzel, M. / Gold, M. / Jones, J.B. / Strynadka, N.C.J.
CitationJournal: 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.
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 1.3Nov 6, 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)29,2692
Polymers28,9421
Non-polymers3271
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.190, 89.280, 42.100
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: 28941.994 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-BJP / (1R)-2-PHENYLACETAMIDO-2-(3-CARBOXYPHENYL)ETHYL BORONIC ACID


Mass: 327.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18BNO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
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: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 2, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 39379 / Num. obs: 14567 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 46.6
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.163 / Num. unique all: 1262 / % possible all: 80.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 18128 / Num. measured all: 73805 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
TNTrefinement
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: bond length = 1.0 bond angle = 1.5 Try planes = 1.2 Gen planes = 4.0 bad contacts 12.0 Temp. = 3.0
RfactorNum. reflection% reflection
Rwork0.181 --
all0.181 11762 -
obs0.181 11762 84 %
Rfree-0 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 34 63 2124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg3.4
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_trig_c_planes0.016
X-RAY DIFFRACTIONt_gen_planes0.02
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 0 / Rfactor all: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2
X-RAY DIFFRACTIONt_planar_d0.012
X-RAY DIFFRACTIONt_plane_restr0.012

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