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

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Basic information

Entry
Database: PDB / ID: 6mia
TitleCrystal structure of CTX-M-14 with compound 6
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / EXBLs / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-INHIBITOR 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-1CE / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.399 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 19, 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7338
Polymers56,0032
Non-polymers1,7306
Water14,070781
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8674
Polymers28,0021
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8674
Polymers28,0021
Non-polymers8653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.340, 107.185, 47.881
Angle α, β, γ (deg.)90.000, 101.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 28001.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: H6UQI0, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical
ChemComp-1CE / 3-(1H-tetrazol-5-ylmethyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4(3H)-one


Mass: 288.328 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H12N6OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.0 M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 86997 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.015 / Rrim(I) all: 0.029 / Χ2: 1.581 / Net I/σ(I): 37.1 / Num. measured all: 315169
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.422.90.04743740.9950.0330.0581.86199.8
1.42-1.453.10.04444210.9960.030.0541.83299.9
1.45-1.483.40.04443660.9960.0280.0531.812100
1.48-1.513.70.04344030.9970.0270.0511.918100
1.51-1.543.70.04143560.9970.0250.0481.856100
1.54-1.583.70.0444130.9970.0240.0461.828100
1.58-1.623.70.03743950.9980.0220.0431.734100
1.62-1.663.70.03443660.9980.020.041.624100
1.66-1.713.70.03244140.9980.0190.0371.566100
1.71-1.763.80.0343750.9990.0180.0351.532100
1.76-1.833.80.02844070.9990.0170.0331.446100
1.83-1.93.80.02644070.9990.0160.0311.468100
1.9-1.993.80.02543770.9990.0150.0291.443100
1.99-2.093.80.02444070.9990.0140.0281.473100
2.09-2.223.80.02243900.9990.0130.0261.355100
2.22-2.393.80.02144360.9990.0130.0251.346100
2.39-2.633.80.02143840.9990.0130.0241.266100
2.63-3.023.70.02144150.9990.0130.0241.28399.6
3.02-3.83.50.02141660.9980.0140.0251.34694.1
3.8-503.20.02737250.9960.0190.0331.9183.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.4 Å22.75 Å
Translation1.4 Å22.75 Å

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Processing

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

1ylt


Resolution: 1.399→22.754 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1633 1994 2.29 %
Rwork0.1249 84971 -
obs0.1258 86965 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.81 Å2 / Biso mean: 12.6989 Å2 / Biso min: 3.47 Å2
Refinement stepCycle: final / Resolution: 1.399→22.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 120 781 4800
Biso mean--27.13 25.27 -
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 (%)
1.3994-1.43440.16051340.09856108624299
1.4344-1.47320.17161360.097861306266100
1.4732-1.51650.15221610.094661026263100
1.5165-1.56550.1411480.093361306278100
1.5655-1.62140.13651380.09761136251100
1.6214-1.68630.14431510.104661246275100
1.6863-1.7630.14751410.115161396280100
1.763-1.85590.16791480.120461306278100
1.8559-1.97220.1651460.122961536299100
1.9722-2.12430.16161380.121261336271100
2.1243-2.33790.17221550.129661416296100
2.3379-2.67580.17561370.136661686305100
2.6758-3.36940.16591430.14346049619299
3.3694-22.75710.17521180.15045351546986

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