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- PDB-6yeo: Crystal structure of AmpC from E. coli with cyclic boronate 2 -

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Basic information

Entry
Database: PDB / ID: 6yeo
TitleCrystal structure of AmpC from E. coli with cyclic boronate 2
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 ...: / : / 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-OK3 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.037 Å
AuthorsLang, P.A. / Schofield, C.J. / Brem, 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 / Category: citation / Item: _citation.title
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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,10921
Polymers158,3524
Non-polymers2,75717
Water15,313850
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3606
Polymers39,5881
Non-polymers7725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1915
Polymers39,5881
Non-polymers6034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2215
Polymers39,5881
Non-polymers6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3375
Polymers39,5881
Non-polymers7494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.683, 179.590, 99.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

21D-692-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ampC, ampA, b4150, JW4111 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P00811, beta-lactamase

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Non-polymers , 7 types, 867 molecules

#2: Chemical
ChemComp-OK3 / (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid


Mass: 357.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18BN2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16 mg/mL AmpC, 20 mM cyclic boronate inhibitor, 0.15 M HEPES pH 7.5, 65 % MDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.03→100.683 Å / Num. obs: 117532 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.995 / Rmerge(I) obs: 0.353 / Rpim(I) all: 0.101 / Rrim(I) all: 0.368 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.03-2.0813.14.17611311486280.6531.1854.3432.8
9.08-100.6711.60.0751724014920.9980.0230.07918.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BLS

2bls


Resolution: 2.037→100.683 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.07
RfactorNum. reflection% reflection
Rfree0.2027 5599 4.89 %
Rwork0.1715 --
obs0.173 114432 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.52 Å2 / Biso mean: 29.0434 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 2.037→100.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10905 0 182 864 11951
Biso mean--41.41 36.13 -
Num. residues----1432
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.037-2.060.32251820.3052331690
2.06-2.08420.33511950.285349897
2.0842-2.10960.28551650.2747356498
2.1096-2.13630.29161910.2624356898
2.1363-2.16440.28272040.2548354198
2.1644-2.19410.27352060.2448354698
2.1941-2.22540.26071800.239355298
2.2254-2.25870.26591680.233360098
2.2587-2.2940.26731950.2205359599
2.294-2.33160.2691960.2252356898
2.3316-2.37180.25241780.209360699
2.3718-2.41490.20542020.2087354999
2.4149-2.46140.21831750.1932362399
2.4614-2.51160.22831860.1854360699
2.5116-2.56620.19492040.182360399
2.5662-2.62590.19671950.1752362599
2.6259-2.69160.2371770.176359199
2.6916-2.76440.21081770.1712366599
2.7644-2.84570.19551850.1692362599
2.8457-2.93760.21711940.1684364999
2.9376-3.04260.19371600.1566366599
3.0426-3.16440.17671750.15043687100
3.1644-3.30840.19891920.14763668100
3.3084-3.48290.17911770.13623697100
3.4829-3.70110.15241740.133704100
3.7011-3.98690.13711740.12273734100
3.9869-4.38810.15441880.11743737100
4.3881-5.0230.15181850.12263745100
5.023-6.32840.19851880.16363795100
6.3284-100.6830.19012310.1876391199
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)
11.1718-0.44860.14471.8850.0310.93050.06090.0808-0.0431-0.0999-0.0005-0.05550.07610.1134-0.05990.132-0.0106-0.04250.158-0.01110.09816.051448.7715102.068
21.84470.10430.11663.304-0.78542.13520.02570.3601-0.0112-0.5912-0.040.0168-0.0513-0.04390.00470.30730.0096-0.06390.23060.02820.1244-5.492562.351687.8965
36.24012.15174.31563.52291.49265.2904-0.13640.35360.1084-0.24960.1233-0.2515-0.33130.39860.00860.183-0.02960.02180.15810.01480.11447.139465.708397.9213
42.2671-1.5291-2.06015.11962.91274.0724-0.09710.10380.0081-0.27860.0785-0.2968-0.00550.4158-0.01860.14470.0119-0.00110.21780.02850.161516.932549.351897.0544
50.8799-0.19510.0681.22340.01160.91170.0060.0373-0.0665-0.04880.02180.07870.0742-0.0405-0.02790.1239-0.0122-0.04060.13740.0080.1103-1.534149.4626105.3401
63.0067-2.72921.33197.00871.73712.7128-0.2506-0.05620.53040.4657-0.11610.1076-0.5090.17510.37060.2172-0.0526-0.01190.22790.00750.507146.390659.6973106.6725
72.3704-0.90770.09221.978500.44160.07040.3226-0.0015-0.0911-0.07220.29190.0427-0.04960.0140.1211-0.0326-0.01750.2386-0.00430.196347.302137.688899.5275
80.55571.09830.52322.25791.08041.31110.07930.8671-0.1282-0.4193-0.2280.2635-0.0228-0.07690.08410.23620.0872-0.04940.5994-0.10980.23561.121526.504286.9924
91.9807-0.82450.11481.7364-0.05691.08790.03820.3171-0.0206-0.0433-0.08140.21940.0428-0.02140.0320.1171-0.0302-0.01520.2245-0.01860.178153.030536.1966100.9942
103.93670.4446-0.25613.28890.16372.9842-0.05290.07220.42280.1144-0.0909-0.0673-0.09520.22290.15520.0932-0.0178-0.01650.13780.00690.258852.422451.495104.9701
116.0495-1.64321.77484.9753-1.24953.11580.15220.39930.39740.050.03450.2766-0.5597-0.1038-0.12740.43120.06220.04950.21510.02410.485816.7678103.6495122.0052
122.06960.6150.03653.4213-1.01481.9389-0.00740.27030.2976-0.2953-0.1025-0.3072-0.24760.13560.10150.20130.01090.01970.16740.00190.203223.773989.5191119.8155
133.4383-1.2631-0.29282.6324-0.93433.71330.01790.0479-0.2430.0452-0.0514-0.40470.3420.2725-0.00570.17960.0231-0.04750.1583-0.02290.272528.494961.4473135.6738
145.9634-1.2080.18572.63230.49253.30230.0327-0.13130.1501-0.0502-0.0309-0.6987-0.04330.47930.01020.15310.0228-0.04050.1964-0.02070.349536.482771.2047138.9707
151.3547-0.21370.50111.478-0.40572.38880.04690.1098-0.0159-0.1113-0.0206-0.24720.12550.2519-0.04420.14690.0243-0.00310.1764-0.03440.25728.261273.2212127.6735
162.60940.76180.00972.3266-0.90252.31180.07170.40760.35-0.3588-0.1249-0.4873-0.14090.41330.03530.2290.00330.07470.21060.00080.304630.113685.4045119.487
173.79331.41382.95384.14572.80837.97620.07540.2039-0.0967-0.10.01870.14820.1193-0.1701-0.09580.116-0.0057-0.01650.1385-0.01630.157111.196372.4624124.4102
183.5688-0.46810.75022.4417-2.84865.0914-0.0112-0.25460.38190.3440.0284-0.095-0.5268-0.0332-0.02050.15720.0014-0.03290.1657-0.06530.219216.742380.6303139.6781
192.1075-0.7950.98651.886-0.22291.452-0.1328-0.3160.51150.2732-0.02-0.2642-0.3566-0.13680.14040.28740.0249-0.05130.2309-0.09880.378720.955691.7504141.5565
200.70080.2815-0.22042.6529-1.29252.119-0.0221-0.02760.21680.06180.016-0.0963-0.2882-0.0818-0.00170.16580.0345-0.03420.1277-0.04350.21817.690989.6811131.1983
215.7449-3.69611.01216.46752.53485.13140.41810.04070.2662-0.2094-0.0956-0.66170.71190.4681-0.31960.68210.03910.23730.19850.00110.515833.0361-13.9167120.5676
220.43380.0488-0.28881.32340.44750.5816-0.50730.2904-0.2392-0.83470.1979-0.45750.33520.1680.08350.6659-0.09540.30530.1334-0.15230.2927.86090.7871116.0538
233.2093-0.1753-0.21252.7122-0.69411.6681-0.0977-0.10520.0719-0.12560.0870.2252-0.068-0.21260.00790.17520.0218-0.03440.1618-0.02840.145716.764322.39131.3287
241.40770.5462-0.25472.36730.22411.1729-0.25370.0683-0.2664-0.4650.0884-0.31810.270.00450.10420.334-0.01320.12470.1457-0.01710.227829.20067.1212124.0124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 102 )A4 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 151 )A103 - 151
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 177 )A152 - 177
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 209 )A178 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 361 )A210 - 361
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 23 )B4 - 23
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 98 )B24 - 98
8X-RAY DIFFRACTION8chain 'B' and (resid 99 through 137 )B99 - 137
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 332 )B138 - 332
10X-RAY DIFFRACTION10chain 'B' and (resid 333 through 361 )B333 - 361
11X-RAY DIFFRACTION11chain 'C' and (resid 4 through 23 )C4 - 23
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 79 )C24 - 79
13X-RAY DIFFRACTION13chain 'C' and (resid 80 through 98 )C80 - 98
14X-RAY DIFFRACTION14chain 'C' and (resid 99 through 137 )C99 - 137
15X-RAY DIFFRACTION15chain 'C' and (resid 138 through 192 )C138 - 192
16X-RAY DIFFRACTION16chain 'C' and (resid 193 through 238 )C193 - 238
17X-RAY DIFFRACTION17chain 'C' and (resid 239 through 256 )C239 - 256
18X-RAY DIFFRACTION18chain 'C' and (resid 257 through 275 )C257 - 275
19X-RAY DIFFRACTION19chain 'C' and (resid 276 through 297 )C276 - 297
20X-RAY DIFFRACTION20chain 'C' and (resid 298 through 361 )C298 - 361
21X-RAY DIFFRACTION21chain 'D' and (resid 4 through 23 )D4 - 23
22X-RAY DIFFRACTION22chain 'D' and (resid 24 through 79 )D24 - 79
23X-RAY DIFFRACTION23chain 'D' and (resid 80 through 162 )D80 - 162
24X-RAY DIFFRACTION24chain 'D' and (resid 163 through 361 )D163 - 361

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