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- PDB-4jxg: Crystal Structure of AmpC beta-lactamase from E. coli in Complex ... -

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Basic information

Entry
Database: PDB / ID: 4jxg
TitleCrystal Structure of AmpC beta-lactamase from E. coli in Complex with Oxacillin
ComponentsBeta-lactamase
Keywordshydrolase/antibiotic / cephalosporinase / beta-lactamase / serine hydrolase / acyl-enzyme complex / hydrolase-antibiotic complex
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
sucrose / Chem-1S6 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWallar, B.J. / Powers, R.A. / Docter, B.E.
CitationJournal: To be Published
Title: Complexed structures of AmpC beta-lactamase
Authors: Docter, B.E. / Baggett, V.L. / Powers, R.A. / Wallar, B.J.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-lactamase
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4206
Polymers79,1762
Non-polymers1,2444
Water10,034557
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0863
Polymers39,5881
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3343
Polymers39,5881
Non-polymers7462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.856, 76.868, 97.845
Angle α, β, γ (deg.)90.00, 117.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


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 / Gene: ampC, ampA, b4150, JW4111 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{}LINUCSPDB-CARE
#3: Chemical ChemComp-1S6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid / Oxacillin, bound form


Mass: 403.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O5S / Comment: antibiotic*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M potassium phosphate, 3.5mg/ml AmpC, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 91996 / % possible obs: 98.9 %
Reflection shellResolution: 1.65→1.71 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.02 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.681 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18457 4614 5 %RANDOM
Rwork0.15077 ---
obs0.15246 87382 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.69 Å2
2--0.16 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 73 557 6160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.025875
X-RAY DIFFRACTIONr_bond_other_d0.0010.025456
X-RAY DIFFRACTIONr_angle_refined_deg2.2351.9588073
X-RAY DIFFRACTIONr_angle_other_deg0.96312526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5745736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64524.516248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64115873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2791526
X-RAY DIFFRACTIONr_chiral_restr0.1350.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021373
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 303 -
Rwork0.221 6109 -
obs--92.58 %

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