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- PDB-6cyu: Crystal structure of CTX-M-14 S70G/N106S/D240G beta-lactamase in ... -

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Basic information

Entry
Database: PDB / ID: 6cyu
TitleCrystal structure of CTX-M-14 S70G/N106S/D240G beta-lactamase in complex with hydrolyzed cefotaxime
ComponentsBeta-lactamase
Keywordshydrolase/antibiotic / Beta-lactamase CTX-M-14 / hydrolase-hydrolase inhibitor complex / hydrolase-antibiotic complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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-CE4 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPatel, M.P. / Hu, L. / Sankaran, B. / Brown, C. / Prasad, B.V.V. / 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: J. Biol. Chem. / Year: 2018
Title: Synergistic effects of functionally distinct substitutions in beta-lactamase variants shed light on the evolution of bacterial drug resistance.
Authors: Patel, M.P. / Hu, L. / Brown, C.A. / Sun, Z. / Adamski, C.J. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionApr 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 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 1.5Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,2992
Polymers27,8851
Non-polymers4131
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.399, 41.399, 230.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Beta-lactamase


Mass: 27885.457 Da / Num. of mol.: 1 / Mutation: S70G, N106S, D240G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AM333_26030, APT94_14605, BET08_34355, BJJ90_27545, BK334_27290, BMR21_24310, BMR35_25520, BMR49_25760, BXT93_06855, CA268_29135, CDL37_21060, CR538_26855, ETN48_p0088, pCT_085, pHK01_011
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9L5C7, UniProt: Q9L5C8*PLUS, beta-lactamase
#2: Chemical ChemComp-CE4 / (2R)-2-[(R)-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro -2H-1,3-thiazine-4-carboxylic acid / cefotaxime, hydrolyzed, C3'-cleaved, open, unbound form


Mass: 413.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.82→35.427 Å / Num. obs: 21719 / % possible obs: 99.78 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.6
Reflection shellResolution: 1.82→1.85 Å / Rmerge(I) obs: 0.106

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Processing

Software
NameVersionClassification
PHENIX(dev_3071: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.82→35.427 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1063 4.89 %
Rwork0.1574 --
obs0.1595 21719 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→35.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 27 281 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062020
X-RAY DIFFRACTIONf_angle_d0.8192751
X-RAY DIFFRACTIONf_dihedral_angle_d7.8781235
X-RAY DIFFRACTIONf_chiral_restr0.05322
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8197-1.90250.25591290.16452524X-RAY DIFFRACTION100
1.9025-2.00280.18731210.15182527X-RAY DIFFRACTION100
2.0028-2.12830.18671310.14822506X-RAY DIFFRACTION100
2.1283-2.29260.20651360.14872574X-RAY DIFFRACTION100
2.2926-2.52330.20231290.16122534X-RAY DIFFRACTION100
2.5233-2.88820.20671410.16712579X-RAY DIFFRACTION100
2.8882-3.63830.19641360.1622629X-RAY DIFFRACTION100
3.6383-35.43370.19131400.15332783X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.32660.4335-0.52330.35930.15231.5507-0.0307-0.0834-0.2002-0.0090.0194-0.02070.55440.33190.04540.20130.0729-0.02560.1523-0.01750.14641.4225-13.0393-15.828
23.323-1.62950.8273.8342-0.98330.92680.14080.16710.14320.0861-0.1406-0.1163-0.6780.502-0.02560.1993-0.12590.00430.3014-0.02970.13799.53611.3702-27.8529
31.16040.5764-0.66440.7544-0.50492.43120.0446-0.1976-0.09160.0272-0.049-0.06080.12680.5917-0.01110.07150.0467-0.01920.2425-0.01070.14085.5812-5.3678-20.4247
48.4341-3.86963.72896.0056-2.1415.6758-0.1087-0.32080.33780.31560.0643-0.04850.0202-0.04030.02330.0950.00750.02990.17770.01030.0565-4.1472-6.2343-6.688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 289 )

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