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- PDB-6v7h: Structure of CTX-M-14 bound to Vaborbactam at 1.0 A -

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Basic information

Entry
Database: PDB / ID: 6v7h
TitleStructure of CTX-M-14 bound to Vaborbactam at 1.0 A
ComponentsBeta-lactamase
KeywordsHYDROLASE / ESBL / boronate / beta-lactamase / inhibitor
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/transpeptidase-like
Similarity search - Domain/homology
Vaborbactam / : / PHOSPHATE ION / Chem-WXM / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 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: 2020
Title: Structural Basis and Binding Kinetics of Vaborbactam in Class A beta-Lactamase Inhibition.
Authors: Pemberton, O.A. / Tsivkovski, R. / Totrov, M. / Lomovskaya, O. / Chen, Y.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)57,55311
Polymers55,9672
Non-polymers1,5869
Water18,8621047
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7295
Polymers27,9841
Non-polymers7454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8246
Polymers27,9841
Non-polymers8405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.300, 106.695, 47.865
Angle α, β, γ (deg.)90.000, 101.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 1056 molecules

#2: Chemical ChemComp-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)- / Vaborbactam


Mass: 297.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16BNO5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-WXM / 2-[(3~{R},6~{S})-2,2-bis(oxidanyl)-3-(2-thiophen-2-ylethanoylamino)-1-oxa-2-boranuidacyclohex-6-yl]ethanoic acid


Mass: 314.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17BNO6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1047 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 39.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→53.36 Å / Num. obs: 228516 / % possible obs: 95.7 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.031 / Rrim(I) all: 0.07 / Rsym value: 0.062 / Net I/σ(I): 13.3
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
1-1.052.80.19887887308840.9390.0230.0580.0535.588.6
3.16-53.366.30.0534849676890.9960.0250.0640.05833.2100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.41 Å46.88 Å
Translation4.41 Å46.88 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.8.1phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UA6

4ua6


Resolution: 1→46.88 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0.63 / Phase error: 9.55
RfactorNum. reflection% reflection
Rfree0.1213 22083 5.2 %
Rwork0.104 --
obs0.1049 228425 89.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.92 Å2 / Biso mean: 10.2493 Å2 / Biso min: 2.85 Å2
Refinement stepCycle: final / Resolution: 1→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 139 1047 5093
Biso mean--15.26 25.12 -
Num. residues----523
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 (%)
1-1.010.1734620.149597861024865
1.01-1.020.15275470.1408111491169674
1.02-1.040.14577120.1301126641337684
1.04-1.050.13697020.1226131721387488
1.05-1.060.13037510.1168132471399888
1.06-1.080.12567370.1129131401387788
1.08-1.090.12187580.1092130081376687
1.09-1.110.11957190.1076128591357886
1.11-1.130.13056350.108122601289582
1.13-1.140.1217470.0959131791392688
1.14-1.160.10457850.0981134591424490
1.16-1.190.11257130.0955135651427890
1.19-1.210.11946860.0977133721405889
1.21-1.230.11827360.0979133041404088
1.23-1.260.12227340.0975130191375386
1.26-1.290.11257160.0956123861310283
1.29-1.320.11358140.0963135571437191
1.32-1.360.11837870.0929137171450492
1.36-1.40.1147900.0942137381452892
1.4-1.440.10598030.0905138141461792
1.44-1.490.10677170.0887138481456592
1.49-1.550.10827020.0919130091371187
1.55-1.620.10947260.0935132531397989
1.62-1.710.10777180.0969146701538897
1.71-1.820.1238110.1029146241543598
1.82-1.960.12128010.1044147411554298
1.96-2.150.11537890.1012149671575699
2.15-2.470.11718280.10381487915707100
2.47-3.110.11897620.10931499915761100
3.11-46.880.14178950.11511488515780100

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