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- PDB-4pm6: Crystal structure of CTX-M-14 S70G beta-lactamase at 1.56 Angstro... -

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Basic information

Entry
Database: PDB / ID: 4pm6
TitleCrystal structure of CTX-M-14 S70G beta-lactamase at 1.56 Angstroms resolution
ComponentsBeta-lactamase CTX-M-14
KeywordsHYDROLASE / class A beta-lactamase
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
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 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 / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
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_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)28,2594
Polymers27,9711
Non-polymers2883
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-42 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.550, 62.280, 86.200
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 BL21(DE3) (bacteria) / References: UniProt: G8XD06, UniProt: A0A0H3H219*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 395 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.56→22.1 Å / Num. obs: 32576 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 39.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.56→22.096 Å / SU ML: 0.12 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 14.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1618 1632 5.02 %
Rwork0.1413 --
obs0.1424 32576 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→22.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 15 395 2372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062003
X-RAY DIFFRACTIONf_angle_d1.0862728
X-RAY DIFFRACTIONf_dihedral_angle_d12.984732
X-RAY DIFFRACTIONf_chiral_restr0.038322
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5601-1.58440.15891250.14152684X-RAY DIFFRACTION100
1.5844-1.61040.15751470.13722622X-RAY DIFFRACTION100
1.6104-1.63820.19961090.13552697X-RAY DIFFRACTION100
1.6382-1.66790.19331320.13872672X-RAY DIFFRACTION100
1.6679-1.70.2271150.1422656X-RAY DIFFRACTION100
1.7-1.73470.18951680.14442668X-RAY DIFFRACTION100
1.7347-1.77240.18211210.14612642X-RAY DIFFRACTION100
1.7724-1.81360.17491180.14132684X-RAY DIFFRACTION100
1.8136-1.85890.18351470.14072634X-RAY DIFFRACTION100
1.8589-1.90920.16871430.13132677X-RAY DIFFRACTION100
1.9092-1.96530.151380.13632666X-RAY DIFFRACTION100
1.9653-2.02870.1761370.1372619X-RAY DIFFRACTION100
2.0287-2.10120.16861470.13822676X-RAY DIFFRACTION100
2.1012-2.18520.15841610.13372644X-RAY DIFFRACTION100
2.1852-2.28460.14611440.13672650X-RAY DIFFRACTION100
2.2846-2.40490.15851760.13672617X-RAY DIFFRACTION100
2.4049-2.55540.14041440.13572627X-RAY DIFFRACTION100
2.5554-2.75230.15921480.14692659X-RAY DIFFRACTION100
2.7523-3.02870.15881270.1432664X-RAY DIFFRACTION100
3.0287-3.46550.12521470.14762672X-RAY DIFFRACTION100
3.4655-4.36070.14081410.13162649X-RAY DIFFRACTION100
4.3607-22.09770.20041500.16672638X-RAY DIFFRACTION100

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