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- PDB-6bu3: CTX-M-27 Beta-Lactamase in Complex with a Non-Covalent Tetrazole ... -

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Basic information

Entry
Database: PDB / ID: 6bu3
TitleCTX-M-27 Beta-Lactamase in Complex with a Non-Covalent Tetrazole Inhibitor
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / tetrazole / inhibitor / beta-lactamase / ESBL / HYDROLASE / hydrolase-hydrolase inhibitor 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-3GK / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Antibacterial Spectrum of a Tetrazole-Based Reversible Inhibitor of Serine beta-Lactamases.
Authors: Pemberton, O.A. / Zhang, X. / Nichols, D.A. / DeFrees, K. / Jaishankar, P. / Bonnet, R. / Adams, J. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,78012
Polymers55,7112
Non-polymers2,07010
Water16,033890
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8906
Polymers27,8551
Non-polymers1,0355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8906
Polymers27,8551
Non-polymers1,0355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.960, 107.240, 47.790
Angle α, β, γ (deg.)90.000, 101.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 27855.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: B5LY47, beta-lactamase
#2: Chemical
ChemComp-3GK / N-[3-(2H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1H-benzimidazole-4-carboxamide


Mass: 373.292 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H10F3N7O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate pH 4.5, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→35.95 Å / Num. all: 156537 / Num. obs: 156537 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 6.92 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.063 / Rrim(I) all: 0.122 / Rsym value: 0.104 / Net I/σ(I): 7.5 / Num. measured all: 567404
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.15-1.213.50.60480031228380.7580.0270.0520.0442.2100
3.64-35.953.60.0441815550380.9960.0290.0570.04920.899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.43 Å35.95 Å
Translation4.43 Å35.95 Å

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Processing

Software
NameVersionClassification
PHENIX1.13rc2_2975refinement
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLP

1ylp


Resolution: 1.15→35.946 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.77 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 13912 5.01 %
Rwork0.1411 263588 -
obs0.1424 277500 89.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.58 Å2 / Biso mean: 12.6974 Å2 / Biso min: 3.57 Å2
Refinement stepCycle: final / Resolution: 1.15→35.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 138 890 4938
Biso mean--16.11 26.9 -
Num. residues----524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16310.26524500.24068207865784
1.1631-1.17680.24034070.23438310871784
1.1768-1.19110.22334110.21628356876785
1.1911-1.20620.2214180.21398325874385
1.2062-1.22210.24033870.2068509889685
1.2221-1.23880.21134220.19988363878586
1.2388-1.25650.22764710.19568396886786
1.2565-1.27530.21444100.198465887586
1.2753-1.29520.21853900.18358617900787
1.2952-1.31640.18914540.17788469892386
1.3164-1.33910.18334900.17098490898087
1.3391-1.36350.19134940.17068684917887
1.3635-1.38970.19474210.15928535895688
1.3897-1.41810.17874970.15198646914388
1.4181-1.44890.18954070.14378837924489
1.4489-1.48260.17174480.1398596904489
1.4826-1.51970.174950.13318745924089
1.5197-1.56080.15484720.12648840931290
1.5608-1.60670.16774840.12868891937590
1.6067-1.65860.15494740.12478881935591
1.6586-1.71780.16024560.12818984944091
1.7178-1.78660.16274540.13499002945692
1.7866-1.86790.1645010.12489051955292
1.8679-1.96640.15945100.129100961093
1.9664-2.08960.13654680.11859229969793
2.0896-2.25090.14384740.12089309978394
2.2509-2.47740.14995720.12799211978395
2.4774-2.83570.15455030.12929440994396
2.8357-3.57220.14525400.118894741001497
3.5722-35.96310.14435320.126296261015898

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