[English] 日本語
Yorodumi
- PDB-4e3o: Crystal structure of AmpC beta-lactamase in complex with a small ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e3o
TitleCrystal structure of AmpC beta-lactamase in complex with a small chloromethyl sulfonamide boronic acid inhibitor
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPC beta-lactamase / class C / cephalosporinase / HYDROLASE-HYDROLASE INHIBITOR complex
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-0NG / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEidam, O. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Fragment-guided design of subnanomolar beta-lactamase inhibitors active in vivo.
Authors: Eidam, O. / Romagnoli, C. / Dalmasso, G. / Barelier, S. / Caselli, E. / Bonnet, R. / Shoichet, B.K. / Prati, F.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9318
Polymers79,1762
Non-polymers7556
Water12,448691
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9654
Polymers39,5881
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9654
Polymers39,5881
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.540, 76.740, 97.880
Angle α, β, γ (deg.)90.000, 116.600, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-0NG / ({[(chloromethyl)sulfonyl]amino}methyl)boronic acid


Mass: 187.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7BClNO4S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.7 M POTASSIUM PHOSPHATE, pH 8.8, vapor diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.6→29.563 Å / Num. obs: 102681 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.217 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.690.5032.43500101553599.7
1.69-1.790.3013.94449621378799.6
1.79-1.910.1826.36426181298899.6
1.91-2.070.10111.12424711292499.5
2.07-2.260.06317.11360921097299.4
2.26-2.530.04722.03344191047499.3
2.53-2.920.03627.9429652910199.2
2.92-3.580.02736.9924885773998.5
3.58-5.10.02144.2719827605199
5.10.01944.8510100311093.8

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 1.6→29.563 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8851 / SU ML: 0.41 / σ(F): 1.99 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 3799 3.7 %
Rwork0.1608 --
obs0.1618 102678 99.36 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.528 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 78.65 Å2 / Biso mean: 25.0627 Å2 / Biso min: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.4873 Å20 Å21.7875 Å2
2--2.486 Å2-0 Å2
3----0.9988 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 40 691 6240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015760
X-RAY DIFFRACTIONf_angle_d1.3057901
X-RAY DIFFRACTIONf_chiral_restr0.089861
X-RAY DIFFRACTIONf_plane_restr0.0071018
X-RAY DIFFRACTIONf_dihedral_angle_d13.3942060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62030.31411500.249736183768100
1.6203-1.64160.2771540.247736893843100
1.6416-1.66410.27641500.241135973747100
1.6641-1.68780.24251530.221936743827100
1.6878-1.7130.25871410.205836443785100
1.713-1.73980.1899880.201537193807100
1.7398-1.76830.20321390.19236723811100
1.7683-1.79880.21951540.188436493803100
1.7988-1.83150.21711500.173836523802100
1.8315-1.86670.21871260.1836803806100
1.8667-1.90480.2057860.174837063792100
1.9048-1.94620.20291350.16623635377099
1.9462-1.99150.20731450.163336673812100
1.9915-2.04130.20961290.154536913820100
2.0413-2.09650.17031490.152236503799100
2.0965-2.15810.20171600.155736473807100
2.1581-2.22780.17451360.15533666380299
2.2278-2.30740.18011300.14963691382199
2.3074-2.39970.20191460.15453653379999
2.3997-2.50890.17631300.15663672380299
2.5089-2.64110.21181480.16333677382599
2.6411-2.80640.18061490.16293650379999
2.8064-3.02290.16741660.16133637380399
3.0229-3.32670.16651460.15813649379599
3.3267-3.80730.15961360.13823655379199
3.8073-4.79340.14331640.129837153879100
4.7934-29.56840.19961390.17123624376396
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)
10.81430.5211-0.09420.806-0.07040.71190.0785-0.1761-0.0050.1263-0.09090.09630.1616-0.11170.00880.1874-0.06130.0110.1412-0.01590.138121.923-9.639224.3951
20.8871-0.0588-0.33651.3782-0.36140.88570.01790.12960.1076-0.1879-0.0259-0.0912-0.01040.01790.00240.1555-0.01670.00510.12070.01130.152538.95239.55187.1515
31.42680.84080.10821.09150.03080.80840.0889-0.180.00580.1615-0.1147-0.03340.0715-0.01050.02350.1406-0.0262-0.0050.1011-0.00420.119331.0461-2.195822.5246
40.5663-0.16630.13960.7989-0.06390.3917-0.03680.0061-0.1683-0.05650.0679-0.16790.30260.5454-0.02840.21090.1157-0.00030.4569-0.01910.20584.0808-13.303621.7766
50.47420.0218-0.12441.22210.20110.8678-0.0046-0.1360.04360.17310.08810.0398-0.09540.1489-0.07840.1642-0.04960.00560.18690.00090.125564.073610.938235.6988
60.719-0.5175-0.03851.0566-0.04881.27740.0027-0.022-0.0155-0.04250.0424-0.02420.10390.2732-0.04110.1049-0.0281-0.01130.196-0.00420.1271.6622-3.430924.2506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:80)A4 - 80
2X-RAY DIFFRACTION2(chain A and resid 81:176)A81 - 176
3X-RAY DIFFRACTION3(chain A and resid 177:361)A177 - 361
4X-RAY DIFFRACTION4(chain B and resid 4:66)B4 - 66
5X-RAY DIFFRACTION5(chain B and resid 67:172)B67 - 172
6X-RAY DIFFRACTION6(chain B and resid 173:361)B173 - 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