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- PDB-6oof: CTX-M-14 Beta Lactamase with Compound 20 -

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Basic information

Entry
Database: PDB / ID: 6oof
TitleCTX-M-14 Beta Lactamase with Compound 20
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / Beta-Lactamase / ESBL / Non covalent 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-R6Z / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.236 Å
AuthorsKemp, M. / 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: Org Chem Front / Year: 2019
Title: An Empirical Study of Amide-Heteroarene pi-Stacking Interactions Using Reversible Inhibitors of a Bacterial Serine Hydrolase.
Authors: DeFrees, K. / Kemp, M.T. / ElHilali-Pollard, X. / Zhang, X. / Mohamed, A. / Chen, Y. / Renslo, A.R.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)57,5726
Polymers55,9672
Non-polymers1,6054
Water12,340685
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7863
Polymers27,9841
Non-polymers8032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7863
Polymers27,9841
Non-polymers8032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.161, 107.211, 47.884
Angle α, β, γ (deg.)90.000, 101.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


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 BL21(DE3) (bacteria)
References: UniProt: A0A2S1PK93, UniProt: Q9L5C7*PLUS, beta-lactamase
#2: Chemical
ChemComp-R6Z / 3-(1H-tetrazol-5-yl)-N-[3-(1H-tetrazol-5-yl)phenyl]-5-(trifluoromethyl)benzamide


Mass: 401.306 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H10F3N9O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 1.0 M potassium phosphate, pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 111033 / % possible obs: 87.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.054 / Rrim(I) all: 0.117 / Χ2: 1.813 / Net I/σ(I): 7.9 / Num. measured all: 467633
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.24-1.263.90.86156950.5660.4650.9850.59989.4
1.26-1.284.30.77457200.6410.4060.8790.61691.4
1.28-1.314.50.71458840.6710.3710.8090.65693.2
1.31-1.344.70.67758660.7150.3440.7640.6992.6
1.34-1.364.80.6358580.7540.3170.7090.69792.7
1.36-1.44.80.59357830.7680.2980.6670.7592.2
1.4-1.434.60.5157140.8050.2620.5770.8490.9
1.43-1.474.20.44455950.8340.2420.5090.92488.4
1.47-1.514.30.37855940.8830.2020.4321.05388.2
1.51-1.564.50.32356150.9090.1690.3671.16789.3
1.56-1.624.40.27755200.9320.1480.3161.38287.6
1.62-1.684.10.23354210.9460.130.2691.57885.6
1.68-1.763.90.19953080.9550.1140.2311.85984.4
1.76-1.853.50.15851680.9670.0960.1862.29481.6
1.85-1.973.10.12148240.9810.0780.1452.95776.3
1.97-2.123.20.09949250.9850.060.1173.78477.8
2.12-2.333.50.08352800.9890.0490.0973.9483.5
2.33-2.6740.07356440.9910.0410.0844.20788.7
2.67-3.374.30.06657140.9930.0340.0754.44290.4
3.37-5050.05859050.9950.0280.0644.21191.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UA6

4ua6


Resolution: 1.236→35.296 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 1988 1.79 %
Rwork0.1708 108933 -
obs0.1714 110921 87.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.53 Å2 / Biso mean: 15.6961 Å2 / Biso min: 6.03 Å2
Refinement stepCycle: final / Resolution: 1.236→35.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 116 685 4708
Biso mean--16.28 26.41 -
Num. residues----523
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 (%)
1.2364-1.26740.29721340.2587561769585
1.2674-1.30160.27831450.24598183832892
1.3016-1.33990.261580.22168275843393
1.3399-1.38320.25431520.218150830292
1.3832-1.43260.19541350.19648130826591
1.4326-1.490.211520.19747799795188
1.49-1.55780.21891400.1877945808589
1.5578-1.63990.21291450.17447767791288
1.6399-1.74270.23281410.17547493763485
1.7427-1.87720.18951290.17127240736981
1.8772-2.06610.20451250.16666734685976
2.0661-2.3650.19361400.16047468760884
2.365-2.97940.18671390.16547960809989
2.9794-35.31030.17091530.14248228838191

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