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- PDB-4pm7: Crystal structure of CTX-M-14 S70G:S237A in complex with cefotaxi... -

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Basic information

Entry
Database: PDB / ID: 4pm7
TitleCrystal structure of CTX-M-14 S70G:S237A in complex with cefotaxime at 1.29 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: 1.29 Å
AuthorsAdamski, C.J. / Cardenas, A.M. / Sankaran, B. / Palzkill, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI32956 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008280 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_assembly / 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_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_related / pdbx_entity_nonpoly / refine_hist
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_related.db_name / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,4102
Polymers27,9551
Non-polymers4551
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint0 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.500, 62.630, 86.140
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: 27954.520 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: S70G, S237A
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.: 413 / 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: 38.57 %
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: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.29→29.4 Å / Num. obs: 56079 / % possible obs: 96.8 % / Redundancy: 2 % / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
iMOSFLM1.0.7data reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementResolution: 1.29→29.4 Å / SU ML: 0.12 / Cross valid method: NONE / σ(F): 1.91 / Phase error: 17.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1839 2807 5 %
Rwork0.1609 --
obs0.162 56079 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 30 413 2404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062022
X-RAY DIFFRACTIONf_angle_d1.1312755
X-RAY DIFFRACTIONf_dihedral_angle_d12.816782
X-RAY DIFFRACTIONf_chiral_restr0.04324
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.29960.22431310.23113167X-RAY DIFFRACTION88
1.2996-1.31490.25721800.21813271X-RAY DIFFRACTION95
1.3149-1.33090.24771530.21593298X-RAY DIFFRACTION94
1.3309-1.34780.20431530.19993364X-RAY DIFFRACTION95
1.3478-1.36550.25241810.20273326X-RAY DIFFRACTION95
1.3655-1.38420.23031640.19723281X-RAY DIFFRACTION94
1.3842-1.4040.21681900.18273329X-RAY DIFFRACTION96
1.404-1.42490.19111830.17883362X-RAY DIFFRACTION95
1.4249-1.44720.1941660.17733327X-RAY DIFFRACTION96
1.4472-1.47090.21351610.17293375X-RAY DIFFRACTION96
1.4709-1.49630.19091840.16973362X-RAY DIFFRACTION96
1.4963-1.52350.17961910.16153345X-RAY DIFFRACTION96
1.5235-1.55280.19191830.16683365X-RAY DIFFRACTION97
1.5528-1.58450.19981830.15773367X-RAY DIFFRACTION96
1.5845-1.6190.16971840.15813403X-RAY DIFFRACTION97
1.619-1.65660.18471960.15893383X-RAY DIFFRACTION96
1.6566-1.6980.20321940.16343359X-RAY DIFFRACTION98
1.698-1.74390.18281800.16123410X-RAY DIFFRACTION97
1.7439-1.79520.19541650.15693400X-RAY DIFFRACTION97
1.7952-1.85320.17571820.15743455X-RAY DIFFRACTION99
1.8532-1.91940.20031900.15673406X-RAY DIFFRACTION98
1.9194-1.99620.17511820.15163435X-RAY DIFFRACTION98
1.9962-2.08710.18031560.15353480X-RAY DIFFRACTION98
2.0871-2.19710.16911680.14663425X-RAY DIFFRACTION98
2.1971-2.33470.16471870.15183479X-RAY DIFFRACTION99
2.3347-2.51480.20691770.15893439X-RAY DIFFRACTION99
2.5148-2.76780.17781890.16383469X-RAY DIFFRACTION99
2.7678-3.16780.19921720.1593388X-RAY DIFFRACTION97
3.1678-3.98960.15521920.14223464X-RAY DIFFRACTION100
3.9896-29.43830.15712150.15143466X-RAY DIFFRACTION100

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