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- PDB-6md8: Crystal structure of CTX-M-14 with compound 3 -

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Basic information

Entry
Database: PDB / ID: 6md8
TitleCrystal structure of CTX-M-14 with compound 3
ComponentsBeta-lactamase CTX-M-14
KeywordsHYDROLASE/INHIBITOR / Tetrazole / inhibitor / complex / Extended spectrum beta-lactamase / 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-J84 / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsAkhtar, 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: Acs Infect Dis. / Year: 2019
Title: Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery.
Authors: Torelli, N.J. / Akhtar, A. / DeFrees, K. / Jaishankar, P. / Pemberton, O.A. / Zhang, X. / Johnson, C. / Renslo, A.R. / Chen, Y.
History
DepositionSep 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Dec 25, 2019Group: Database references / Category: struct_ref_seq_dif
Revision 2.2Oct 11, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,0127
Polymers55,9672
Non-polymers1,0455
Water13,169731
1
A: Beta-lactamase CTX-M-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6544
Polymers27,9841
Non-polymers6703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase CTX-M-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3583
Polymers27,9841
Non-polymers3742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.202, 106.878, 47.781
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase CTX-M-14


Mass: 27983.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-14 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S1PK93, UniProt: Q9L5C7*PLUS
#2: Chemical ChemComp-J84 / 1-(2,4-dichlorophenyl)-4-(1H-tetrazol-5-yl)-1H-pyrazol-5-amine


Mass: 296.115 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H7Cl2N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 39.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1 M Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 86617 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.019 / Rrim(I) all: 0.036 / Χ2: 2.274 / Net I/σ(I): 34.7 / Num. measured all: 308974
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.422.90.0642790.9920.0430.0742.36898.8
1.42-1.453.10.05743940.9930.0390.0692.38899.7
1.45-1.483.30.05843100.9940.0380.0692.48899.8
1.48-1.513.60.05643920.9950.0350.0662.64199.9
1.51-1.543.60.05443450.9950.0330.0632.62799.7
1.54-1.583.60.05143160.9960.0320.062.57399.8
1.58-1.623.60.04743580.9960.0290.0552.52399.9
1.62-1.663.70.04543500.9960.0280.0532.5199.9
1.66-1.713.70.04243700.9970.0260.0492.36999.9
1.71-1.763.70.0443700.9970.0240.0472.40199.9
1.76-1.833.70.03743450.9970.0230.0432.29699.9
1.83-1.93.70.03543790.9980.0210.0412.3299.8
1.9-1.993.70.03343530.9980.020.0382.29399.8
1.99-2.093.70.0343590.9980.0180.0362.20899.8
2.09-2.223.70.02943410.9980.0180.0342.20499.9
2.22-2.393.70.02743990.9990.0160.0312.01799.9
2.39-2.633.80.02543690.9990.0150.0291.86999.9
2.63-3.023.70.02443880.9990.0140.0281.77399.9
3.02-3.83.50.02442420.9980.0150.0281.68896.8
3.8-503.30.02739580.9970.0190.0331.9588.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.4 Å23.38 Å
Translation1.4 Å23.38 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3228refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt


Resolution: 1.4→23.378 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.96
RfactorNum. reflection% reflection
Rfree0.1694 1994 2.3 %
Rwork0.1481 --
obs0.1486 86586 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.99 Å2 / Biso mean: 11.1128 Å2 / Biso min: 2.99 Å2
Refinement stepCycle: final / Resolution: 1.4→23.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 73 731 4703
Biso mean--12.89 21.26 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3969-1.43180.151280.14465826595495
1.4318-1.47050.19631550.146360536208100
1.4705-1.51380.16941350.144660856220100
1.5138-1.56260.16871410.143960826223100
1.5626-1.61850.17451510.138360996250100
1.6185-1.68330.16541520.141461016253100
1.6833-1.75980.17861460.151660846230100
1.7598-1.85260.16761360.151160896225100
1.8526-1.96860.18031440.145861146258100
1.9686-2.12050.14921490.149260816230100
2.1205-2.33370.15031420.145861336275100
2.3337-2.6710.17361430.15361266269100
2.671-3.36360.17691430.15256074621799
3.3636-23.38120.17521290.14825645577491

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