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- PDB-3bls: AMPC BETA-LACTAMASE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 3bls
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
M-AMINOPHENYLBORONIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 2.3 Å
AuthorsUsher, K.C. / Shoichet, B.K. / 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 4, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,4504
Polymers79,1762
Non-polymers2742
Water1,928107
1
A: AMPC BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,5881
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AMPC BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7252
Polymers39,5881
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.380, 78.970, 99.300
Angle α, β, γ (deg.)90.00, 116.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99824, 0.058222, -0.011253), (0.059293, 0.977254, -0.203615), (-0.000858, -0.203924, -0.978986)
Vector: 103.5614, 1.68154, 46.09845)

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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: Chemical ChemComp-APB / M-AMINOPHENYLBORONIC ACID


Mass: 136.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8BNO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.7
Details: PROTEIN WAS CRYSTALLIZED FROM 1.7M NA/K PHOSPHATE, PH 8.7, COCRYSTALLIZED IN THE PRESENCE OF MAPB INHIBITOR. 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: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 35225 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3
Reflection
*PLUS
Num. all: 36886 / Num. measured all: 114023
Reflection shell
*PLUS
% possible obs: 88.3 % / Num. possible: 7324 / Num. unique obs: 6468

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Processing

Software
NameClassification
TNTrefinement
UCSDdata reduction
UCSDdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR SUBSTITUTION
Starting model: PDB ENTRY 2BLS

2bls


Resolution: 2.3→25 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.159 --
all0.216 35707 -
obs0.159 35707 96 %
Rfree-0 -
Solvent computationSolvent model: BABINET SCALING / Bsol: 531 Å2 / ksol: 0.99 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 20 107 5707
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01957621
X-RAY DIFFRACTIONt_angle_deg2.6978242
X-RAY DIFFRACTIONt_dihedral_angle_d18.433080
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0131382
X-RAY DIFFRACTIONt_gen_planes0.0198205
X-RAY DIFFRACTIONt_it8.0157680.5
X-RAY DIFFRACTIONt_nbd0.02310120
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.40
X-RAY DIFFRACTIONt_planar_d0.0132
X-RAY DIFFRACTIONt_plane_restr0.0195

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