[English] 日本語
Yorodumi
- PDB-6yeo: Crystal structure of AmpC from E. coli with cyclic boronate 2 -

+
Open data


ID or keywords:

Loading...

-
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 / beta-lactamase activity / outer membrane-bounded periplasmic space / periplasmic space
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more