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- PDB-6ooe: CTX-M-27 Beta Lactamase with Compound 20 -

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Basic information

Entry
Database: PDB / ID: 6ooe
TitleCTX-M-27 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
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 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)57,5386
Polymers55,9332
Non-polymers1,6054
Water13,133729
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7693
Polymers27,9671
Non-polymers8032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7693
Polymers27,9671
Non-polymers8032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.323, 107.482, 48.057
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 27966.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-27, CTX-M-14like / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7AP60, 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: obtained synthetically / Formula: C16H10F3N9O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion / 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 206742 / % possible obs: 99.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 25.17
Reflection shellResolution: 1.26→1.28 Å / Rmerge(I) obs: 0.674 / Num. unique obs: 5279 / % possible all: 94.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ua6

4ua6


Resolution: 1.26→34.27 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 2010 1.86 %
Rwork0.145 105913 -
obs0.1454 107923 89.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.69 Å2 / Biso mean: 14.0124 Å2 / Biso min: 5.32 Å2
Refinement stepCycle: final / Resolution: 1.26→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 116 729 4756
Biso mean--14.71 25.92 -
Num. residues----524
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 (%)
1.2603-1.29180.20191340.17467331746587
1.2918-1.32680.2051440.1557511765589
1.3268-1.36580.18781480.1437432758088
1.3658-1.40990.17311480.13657381752988
1.4099-1.46030.17241310.1337289742086
1.4603-1.51880.17231430.12837362750587
1.5188-1.58790.16411460.11887782792892
1.5879-1.67160.14851480.11927806795492
1.6716-1.77630.17451500.12987813796392
1.7763-1.91350.20591370.13987572770989
1.9135-2.1060.1431450.13847370751587
2.106-2.41070.15151430.14567806794992
2.4107-3.03690.19111510.16277802795392
3.0369-34.28280.17141420.15527656779889

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