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- PDB-6yen: Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133) -

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Basic information

Entry
Database: PDB / ID: 6yen
TitleCrystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase / antibiotic resistance / bicyclic boronate
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-K9K / Chem-KJK / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.418 Å
AuthorsLang, P.A. / Brem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MRF-145-0004-TPG-AVISO United Kingdom
CitationJournal: Biomolecules / Year: 2020
Title: Bicyclic Boronates as Potent Inhibitors of AmpC, the Class C beta-Lactamase from Escherichia coli .
Authors: Lang, P.A. / Parkova, A. / Leissing, T.M. / Calvopina, K. / Cain, R. / Krajnc, A. / Panduwawala, T.D. / Philippe, J. / Fishwick, C.W.G. / Trapencieris, P. / Page, M.G.P. / Schofield, C.J. / Brem, J.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Jan 24, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,11314
Polymers39,5881
Non-polymers1,52513
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-81 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.229, 137.229, 137.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-408-

ZN

21A-410-

CL

31A-789-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00811, beta-lactamase

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Non-polymers , 9 types, 358 molecules

#2: Chemical ChemComp-KJK / (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 389.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-K9K / (10aR)-2-(((1r,4R)-4-((2-aminoethyl)amino)cyclohexyl)methyl)-6-carboxy-4-hydroxy-4,10a-dihydro-10H-benzo[5,6][1,2]oxaborinino[2,3-b][1,4,2]oxazaborol-4-uide


Mass: 388.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27BN3O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 15 % PEG6000, 0.01 M ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.418→97.04 Å / Num. obs: 83520 / % possible obs: 100 % / Redundancy: 76.8 % / CC1/2: 1 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.015 / Rrim(I) all: 0.135 / Net I/σ(I): 26.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.42-1.578.66.3781119930.4410.7226.419
4.49-97.0467.50.044113.9296610.0050.044

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.69 Å97.04 Å
Translation5.69 Å97.04 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.3phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEM

1iem


Resolution: 1.418→97.036 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.88
RfactorNum. reflection% reflection
Rfree0.1687 4112 4.93 %
Rwork0.1442 --
obs0.1454 83425 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.32 Å2 / Biso mean: 28.3698 Å2 / Biso min: 13.74 Å2
Refinement stepCycle: final / Resolution: 1.418→97.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 89 349 3186
Biso mean--44.06 39.49 -
Num. residues----358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4184-1.43510.32541230.2692691
1.4351-1.45260.2911390.27122670
1.4526-1.4710.32191330.24852704
1.471-1.49040.28281370.24052682
1.4904-1.51080.24881350.22812689
1.5108-1.53240.21941030.21512755
1.5324-1.55520.22721510.19182684
1.5552-1.57960.2191450.17852691
1.5796-1.60550.1961530.17392673
1.6055-1.63310.1991600.15622711
1.6331-1.66280.20771460.14582665
1.6628-1.69480.20791270.1452743
1.6948-1.72940.19251480.13462682
1.7294-1.7670.17251380.13062713
1.767-1.80810.18421530.12852729
1.8081-1.85340.18771440.12292693
1.8534-1.90350.18491300.1222738
1.9035-1.95950.17971590.12172706
1.9595-2.02270.13491150.11882742
2.0227-2.0950.16151410.12212716
2.095-2.17890.14981520.1222745
2.1789-2.27810.14351470.12072733
2.2781-2.39820.1391360.12032763
2.3982-2.54850.16691490.13022752
2.5485-2.74530.17061410.13962782
2.7453-3.02150.16291430.14572770
3.0215-3.45880.17351490.14962804
3.4588-4.35770.13371660.12722839
4.3577-97.0360.17971490.16713048

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