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- PDB-2bls: AMPC BETA-LACTAMASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 2bls
TitleAMPC BETA-LACTAMASE FROM ESCHERICHIA COLI
ComponentsAMPC BETA-LACTAMASE
KeywordsCEPHALOSPORINASE / BETA-LACTAMASE / SERINE HYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUsher, K.C. / Wery, J.-P. / Blaszczak, L.C. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1998
Title: Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design.
Authors: Usher, K.C. / Blaszczak, L.C. / Weston, G.S. / Shoichet, B.K. / Remington, S.J.
History
DepositionJun 3, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMPC BETA-LACTAMASE
B: AMPC BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)79,1762
Polymers79,1762
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.730, 77.350, 97.590
Angle α, β, γ (deg.)90.00, 116.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997453, 0.070717, 0.00935), (0.067323, 0.976591, -0.204295), (-0.023578, -0.203145, -0.978865)
Vector: 100.98057, 1.18085, 46.77961)

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Components

#1: Protein AMPC BETA-LACTAMASE


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: PERIPLASM / Gene: AMPC / Plasmid: POG0295 / Cellular location (production host): EXTRACELLULAR / Gene (production host): AMPC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.7
Details: PROTEIN WAS CRYSTALLIZED FROM 1.7M NA/K PHOSPHATE, PH 8.7. LARGER CRYSTALS WERE GROWN BY MICRO-SEEDING TECHNIQUE
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 8.7 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Msodium potassium phosphate1reservoir
210 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 41301 / % possible obs: 77.4 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.25 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 3.1 / % possible all: 58.1
Reflection
*PLUS
Num. all: 52822 / Num. measured all: 73349 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 58.1 % / Num. possible: 15650 / Num. unique obs: 9094

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Frefinement
MSCdata reduction
MSCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BLT

2blt
PDB Unreleased entry


Resolution: 2→25 Å / Isotropic thermal model: TNT BCORREL / σ(F): 1 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.216 --
obs0.216 41301 77.4 %
Rfree-0 -
all-41301 -
Solvent computationSolvent model: BABINET SCALING / Bsol: 149 Å2 / ksol: 0.87 e/Å3
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 0 82 5662
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01957391
X-RAY DIFFRACTIONt_angle_deg2.8277882
X-RAY DIFFRACTIONt_dihedral_angle_d19.233100
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0141372
X-RAY DIFFRACTIONt_gen_planes0.0188185
X-RAY DIFFRACTIONt_it7.7657390.5
X-RAY DIFFRACTIONt_nbd0.02712920
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.20
X-RAY DIFFRACTIONt_planar_d0.0142
X-RAY DIFFRACTIONt_plane_restr0.0185

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