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- PDB-3ixb: X-ray crystal structure of the extended-spectrum AmpC E219K mutan... -

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Basic information

Entry
Database: PDB / ID: 3ixb
TitleX-ray crystal structure of the extended-spectrum AmpC E219K mutant beta-lactamase complexed with benzo(b)thiophene-2-boronic acid (BZB) at 1.63 Angstrom resolution
ComponentsBeta-lactamase
KeywordsHYDROLASE / serine hydrolase / beta-lactamase / cephalosporinase / extended-spectrum antibiotic resistance / Antibiotic resistance / Periplasm
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
BENZO[B]THIOPHENE-2-BORONIC ACID / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsShoichet, B.K. / Thomas, V.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural bases for stability-function tradeoffs in antibiotic resistance.
Authors: Thomas, V.L. / McReynolds, A.C. / Shoichet, B.K.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)79,7226
Polymers79,1762
Non-polymers5464
Water15,439857
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8613
Polymers39,5881
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8613
Polymers39,5881
Non-polymers2732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.061, 77.412, 97.235
Angle α, β, γ (deg.)90.00, 115.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.988 Da / Num. of mol.: 2 / Mutation: E219K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BZB / BENZO[B]THIOPHENE-2-BORONIC ACID


Mass: 178.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7BO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M KPi, pH 8.7, 360 uM benzo(b)thiophene-2-boronic acid, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2009 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.63→87.702 Å / Num. all: 97618 / Num. obs: 97467 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rsym value: 0.061

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.82 Å58.39 Å
Translation1.82 Å58.39 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KE4

1ke4


Resolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 1.522 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20758 4868 5 %RANDOM
Rwork0.17657 ---
obs0.17811 92583 99.85 %-
all-97618 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.13 Å2
2--0.15 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 34 857 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9547911
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68324.628242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2715915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8231523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214433
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6631.53569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25325762
X-RAY DIFFRACTIONr_scbond_it2.11832218
X-RAY DIFFRACTIONr_scangle_it3.5344.52148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 350 -
Rwork0.293 6844 -
obs--99.97 %

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