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- PDB-6ypd: Crystal structure of AmpC from E. coli with Cyclic Boronate 3 (CB... -

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Basic information

Entry
Database: PDB / ID: 6ypd
TitleCrystal structure of AmpC from E. coli with Cyclic Boronate 3 (CB3 / APC308)
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-KL8 / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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
DepositionApr 15, 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 / struct_conn / struct_conn_type
Item: _citation.title / _struct_conn.conn_type_id ..._citation.title / _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_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_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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4349
Polymers39,5881
Non-polymers8478
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-30 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.971, 138.971, 138.971
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-407-

CL

21A-408-

ZN

31A-804-

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 str. K-12 substr. W3110 (bacteria)
References: UniProt: P00811, beta-lactamase

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Non-polymers , 7 types, 364 molecules

#2: Chemical ChemComp-KL8 / (3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid


Mass: 331.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16BO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25% (w/v) PEG6000, 0.01 M ZnCl2, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.599→138.97 Å / Num. obs: 60941 / % possible obs: 100 % / Redundancy: 77.3 % / CC1/2: 1 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.019 / Rrim(I) all: 0.166 / Net I/σ(I): 22.1
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.6-1.6367.44.5041.329480.6730.5474.538
8.76-138.9763.40.03976.948110.0050.04

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.66 Å98.32 Å
Translation5.66 Å98.32 Å

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimless0.7.4data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEM

1iem


Resolution: 1.6→49.134 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.8
RfactorNum. reflection% reflection
Rfree0.1874 1990 3.28 %
Rwork0.1709 --
obs0.1715 60656 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.06 Å2 / Biso mean: 31.0051 Å2 / Biso min: 14.68 Å2
Refinement stepCycle: final / Resolution: 1.6→49.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 50 376 3190
Biso mean--57.38 40.61 -
Num. residues----358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.63890.28281400.23924127100
1.6389-1.68330.25921410.21154129100
1.6833-1.73280.25081400.20344128100
1.7328-1.78870.22631400.19744125100
1.7887-1.85270.23171410.1874158100
1.8527-1.92680.27791390.2659407998
1.9268-2.01450.20611380.1896411599
2.0145-2.12070.2031380.19374136100
2.1207-2.25360.19791420.1868416699
2.2536-2.42760.2011420.16924179100
2.4276-2.67190.1851430.15554214100
2.6719-3.05850.17611450.15494259100
3.0585-3.85310.15131470.15764310100
3.8531-49.1340.17081540.15494541100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.672-0.8965-1.35476.6841.38783.14560.06230.1534-0.0423-0.3345-0.1838-0.16630.0962-0.09720.1150.21070.01190.01830.24390.00540.1926-3.1991-0.47656.4347
23.0720.8659-2.11991.4098-0.56182.21410.1235-0.20610.11340.1224-0.0216-0.0951-0.11250.1507-0.11690.16650.0013-0.02750.13720.00890.1339-5.31292.855823.0206
31.3691-0.09920.5953.4195-0.89650.5930.1357-0.24990.27010.5172-0.01520.3252-0.2855-0.2705-0.10570.39690.04740.16640.2862-0.01650.2849-30.52878.370943.7818
41.7873-0.3443-0.65432.41840.36893.54650.272-0.11540.50630.35260.05780.0906-0.7504-0.2787-0.18990.39010.07380.16260.22070.00890.2992-27.798416.561834.1821
52.19370.6703-0.95221.0278-0.13991.28890.0363-0.15770.01810.1915-0.0209-0.037-0.07430.0809-0.0140.2319-0.00020.00760.17340.0040.1555-13.57151.632731.0669
61.6383-0.0809-0.84770.6974-0.31021.6285-0.00570.22940.01060.00080.04310.1326-0.0088-0.2732-0.03820.19090.00250.00210.21090.00780.1828-18.47171.88215.695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )A4 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 79 )A24 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 98 )A80 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 162 )A99 - 162
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 275 )A163 - 275
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 362 )A276 - 362

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