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- PDB-6ka5: Crystal structure of a class C beta-lactamase in complex with cef... -

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Basic information

Entry
Database: PDB / ID: 6ka5
TitleCrystal structure of a class C beta-lactamase in complex with cefoxitin
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class C-lactamase / Acyl-enzyme 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
Chem-1S7 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsBae, D.W. / Jung, Y.E. / An, Y.J. / Na, J.H. / Cha, S.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Structural Insights into Catalytic Relevances of Substrate Poses in ACC-1.
Authors: Bae, D.W. / Jung, Y.E. / An, Y.J. / Na, J.H. / Cha, S.S.
History
DepositionJun 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Oct 12, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / database_2 / diffrn_radiation_wavelength / diffrn_source / entity / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_mon_prot_cis / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _database_2.pdbx_DOI ..._cell.volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity.pdbx_number_of_molecules / _pdbx_contact_author.id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_poly_seq_scheme.auth_mon_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.name / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
Description: Ligand geometry
Details: Ligand was not covalently linked to the amino acid no.64 Serine in the previously deposited coordination file, so I further modeled the ligand to be linked to the Ser64.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 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
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0822
Polymers40,7131
Non-polymers3681
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14670 Å2
Unit cell
Length a, b, c (Å)133.092, 60.340, 56.490
Angle α, β, γ (deg.)90.000, 111.930, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Beta-lactamase /


Mass: 40713.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla-ACC-1, acc-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XB24, beta-lactamase
#2: Chemical ChemComp-1S7 / (2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cefoxitin, bound form / Cefoxitin


Mass: 368.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N2O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.1M sodium cacodylate pH 5.5 0.2M sodium chloride 35% polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.586→50 Å / Num. obs: 52020 / % possible obs: 92.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 10.54 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.033 / Rrim(I) all: 0.077 / Χ2: 4.073 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.59-1.624.20.21326620.960.1150.2433.29295.7
1.62-1.654.50.18927460.9720.0990.2143.41798.9
1.65-1.684.60.1627510.980.0830.1813.57798.9
1.68-1.714.70.15527860.9820.0790.1753.48598.7
1.71-1.754.70.13827310.9840.070.1553.59898.2
1.75-1.794.60.12627460.9840.0640.1423.76898.6
1.79-1.845.10.11428100.9890.0540.1263.72399.5
1.84-1.895.20.10927820.9890.0520.1214.00899.6
1.89-1.944.10.10214870.990.0530.1164.08853.2
1.94-24.90.08927840.9920.0440.14.37699.2
2-2.074.60.08427570.9920.0430.0954.57398.6
2.07-2.1650.07927940.9930.0380.0884.55499.5
2.16-2.264.90.07621510.9930.0360.0844.60177
2.26-2.3850.07422650.9930.0360.0834.62180
2.38-2.525.20.07127780.9940.0340.0794.6298.7
2.52-2.725.10.0727690.9930.0330.0784.72998.8
2.72-2.995.70.06627980.9950.0290.0734.51899.6
2.99-3.435.60.0628160.9960.0270.0664.25799.4
3.43-4.324.80.05317460.9950.0250.0593.91961.1
4.32-505.70.05128610.9970.0230.0563.49898.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXH

3ixh


Resolution: 1.59→41.21 Å / SU ML: 0.1517 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 17.9439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1913 1995 3.85 %
Rwork0.1587 49793 -
obs0.16 51788 92.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.69 Å2
Refinement stepCycle: LAST / Resolution: 1.59→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 24 449 3191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852801
X-RAY DIFFRACTIONf_angle_d1.06283809
X-RAY DIFFRACTIONf_chiral_restr0.0657436
X-RAY DIFFRACTIONf_plane_restr0.0065483
X-RAY DIFFRACTIONf_dihedral_angle_d17.03711032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.27171550.20693722X-RAY DIFFRACTION97.88
1.63-1.670.22081530.17593761X-RAY DIFFRACTION98.94
1.67-1.720.20211460.17943801X-RAY DIFFRACTION98.48
1.72-1.780.19761610.16813731X-RAY DIFFRACTION98.26
1.78-1.840.21251410.15573819X-RAY DIFFRACTION99.57
1.84-1.910.20511240.15473282X-RAY DIFFRACTION96.19
1.93-20.19991330.15623065X-RAY DIFFRACTION93.65
2-2.110.17751420.15593795X-RAY DIFFRACTION98.87
2.11-2.230.20061370.15363489X-RAY DIFFRACTION95.47
2.27-2.410.19621230.15813007X-RAY DIFFRACTION95.69
2.41-2.660.19221500.15993788X-RAY DIFFRACTION98.57
2.66-3.040.17281550.16243858X-RAY DIFFRACTION99.5
3.04-3.830.18061330.15343059X-RAY DIFFRACTION79.62
3.83-41.210.17271420.14593616X-RAY DIFFRACTION91.61

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