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- PDB-4pm5: Crystal structure of CTX-M-14 S70G beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4pm5
TitleCrystal structure of CTX-M-14 S70G beta-lactamase in complex with cefotaxime at 1.26 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 / MOLECULAR REPLACEMENT / Resolution: 1.261 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_close_contact
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 1.5Sep 27, 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_entity_nonpoly / pdbx_initial_refinement_model / 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_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)28,7145
Polymers27,9711
Non-polymers7444
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-10 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.550, 62.680, 86.130
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: 27970.520 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: S70G
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 38.65 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Ammonium phosphate, 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: 1.26→29.5 Å / Num. obs: 61202 / % possible obs: 99.7 % / Redundancy: 2 % / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
iMOSFLM1.0.7data reduction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.261→29.451 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 16.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 3046 4.98 %
Rwork0.1617 --
obs0.1627 61202 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.261→29.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 45 405 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052035
X-RAY DIFFRACTIONf_angle_d1.1322774
X-RAY DIFFRACTIONf_dihedral_angle_d12.571783
X-RAY DIFFRACTIONf_chiral_restr0.039324
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.261-1.27530.21871620.21653577X-RAY DIFFRACTION96
1.2753-1.29030.19552010.20433662X-RAY DIFFRACTION99
1.2903-1.30610.23322020.20263674X-RAY DIFFRACTION99
1.3061-1.32260.21511850.19913641X-RAY DIFFRACTION99
1.3226-1.340.21841690.19523729X-RAY DIFFRACTION99
1.34-1.35840.21582000.18983664X-RAY DIFFRACTION99
1.3584-1.37780.19382020.193715X-RAY DIFFRACTION100
1.3778-1.39830.19822410.18063589X-RAY DIFFRACTION99
1.3983-1.42020.16991980.16873729X-RAY DIFFRACTION100
1.4202-1.44350.17471760.16353695X-RAY DIFFRACTION99
1.4435-1.46840.21131870.16953710X-RAY DIFFRACTION99
1.4684-1.49510.17691770.16523673X-RAY DIFFRACTION99
1.4951-1.52380.18461930.16163684X-RAY DIFFRACTION100
1.5238-1.55490.18751740.16193726X-RAY DIFFRACTION100
1.5549-1.58870.191930.16283737X-RAY DIFFRACTION100
1.5887-1.62570.16892040.15453668X-RAY DIFFRACTION100
1.6257-1.66630.17941930.15493738X-RAY DIFFRACTION100
1.6663-1.71140.16761900.15943680X-RAY DIFFRACTION100
1.7114-1.76170.19851830.15783712X-RAY DIFFRACTION100
1.7617-1.81860.20032040.15213708X-RAY DIFFRACTION100
1.8186-1.88360.1831900.16023728X-RAY DIFFRACTION100
1.8836-1.9590.16171910.15163705X-RAY DIFFRACTION100
1.959-2.04810.15581860.15593732X-RAY DIFFRACTION100
2.0481-2.15610.15261770.14743718X-RAY DIFFRACTION100
2.1561-2.29110.16661980.15273705X-RAY DIFFRACTION100
2.2911-2.46790.2211800.16263703X-RAY DIFFRACTION100
2.4679-2.71610.1921970.16563729X-RAY DIFFRACTION100
2.7161-3.10880.18452360.15983640X-RAY DIFFRACTION100
3.1088-3.91530.16282050.14583717X-RAY DIFFRACTION100
3.9153-29.45890.17752130.16093672X-RAY DIFFRACTION100

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