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- PDB-4pm9: Crystal structure of CTX-M-14 S70G:S237A:R276A beta-lactamase in ... -

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Basic information

Entry
Database: PDB / ID: 4pm9
TitleCrystal structure of CTX-M-14 S70G:S237A:R276A beta-lactamase in complex with cefotaxime at 1.45 Angstroms resolution
ComponentsBeta-lactamase CTX-M-14
KeywordsHYDROLASE/ANTIBIOTIC / Class A beta-lactamase / cefotaxime / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CE3 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.454 Å
AuthorsCardenas, A.M. / Adamski, C.J. / Sankaran, B. / Brown, N.G. / Horton, L.B. / Palzkill, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI32956 United States
CitationJournal: Biochemistry / Year: 2015
Title: Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum beta-Lactamases.
Authors: Adamski, C.J. / Cardenas, A.M. / Brown, N.G. / Horton, L.B. / Sankaran, B. / Prasad, B.V. / Gilbert, H.F. / Palzkill, T.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 30, 2021Group: Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase CTX-M-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1962
Polymers27,7401
Non-polymers4551
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-0 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.530, 61.737, 86.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase CTX-M-14


Mass: 27740.275 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: HS11286 / Gene: KPHS_p301310 / Production host: Escherichia coli (E. coli) / References: UniProt: G8XD06, UniProt: A0A0H3H219*PLUS
#2: Chemical ChemComp-CE3 / (6R,7R)-3-(acetyloxymethyl)-7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methoxyimino-ethanoyl]amino]-8-oxo-5-thia-1-azabicy clo[4.2.0]oct-2-ene-2-carboxylic acid / CEFOTAXIME


Mass: 455.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N5O7S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→37.5 Å / Num. obs: 41240 / % possible obs: 98.9 % / Redundancy: 2.7 % / Net I/σ(I): 22.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementResolution: 1.454→37.453 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 0 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 1971 5.02 %
Rwork0.1609 --
obs0.1619 39269 98.19 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.65 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2341 Å2-0 Å20 Å2
2--0.3309 Å20 Å2
3---0.9032 Å2
Refinement stepCycle: LAST / Resolution: 1.454→37.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 30 305 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052012
X-RAY DIFFRACTIONf_angle_d1.122745
X-RAY DIFFRACTIONf_dihedral_angle_d12.951777
X-RAY DIFFRACTIONf_chiral_restr0.065324
X-RAY DIFFRACTIONf_plane_restr0.005361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.454-1.50590.21162020.19593525X-RAY DIFFRACTION94
1.5059-1.56620.19731750.1643604X-RAY DIFFRACTION96
1.5662-1.63750.1791740.15573659X-RAY DIFFRACTION97
1.6375-1.72380.18461950.15573681X-RAY DIFFRACTION98
1.7238-1.83180.16991810.15893699X-RAY DIFFRACTION99
1.8318-1.97330.20971790.16063797X-RAY DIFFRACTION99
1.9733-2.17180.1831980.16183765X-RAY DIFFRACTION100
2.1718-2.4860.17472330.15963768X-RAY DIFFRACTION100
2.486-3.13190.18412020.17283816X-RAY DIFFRACTION99
3.1319-37.46510.16732320.15143984X-RAY DIFFRACTION100

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