[English] 日本語
Yorodumi
- PDB-6bu3: CTX-M-27 Beta-Lactamase in Complex with a Non-Covalent Tetrazole ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bu3
TitleCTX-M-27 Beta-Lactamase in Complex with a Non-Covalent Tetrazole Inhibitor
ComponentsBeta-lactamase
Keywordshydrolase/hydrolase inhibitor / tetrazole / inhibitor / beta-lactamase / ESBL / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3GK / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Antibacterial Spectrum of a Tetrazole-Based Reversible Inhibitor of Serine beta-Lactamases.
Authors: Pemberton, O.A. / Zhang, X. / Nichols, D.A. / DeFrees, K. / Jaishankar, P. / Bonnet, R. / Adams, J. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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

-
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)57,78012
Polymers55,7112
Non-polymers2,07010
Water16,033890
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8906
Polymers27,8551
Non-polymers1,0355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8906
Polymers27,8551
Non-polymers1,0355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.960, 107.240, 47.790
Angle α, β, γ (deg.)90.000, 101.860, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-lactamase /


Mass: 27855.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: B5LY47, beta-lactamase
#2: Chemical
ChemComp-3GK / N-[3-(2H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1H-benzimidazole-4-carboxamide


Mass: 373.292 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H10F3N7O
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate pH 4.5, 1.6 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→35.95 Å / Num. all: 156537 / Num. obs: 156537 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 6.92 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.063 / Rrim(I) all: 0.122 / Rsym value: 0.104 / Net I/σ(I): 7.5 / Num. measured all: 567404
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.15-1.213.50.60480031228380.7580.0270.0520.0442.2100
3.64-35.953.60.0441815550380.9960.0290.0570.04920.899.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.43 Å35.95 Å
Translation4.43 Å35.95 Å

-
Processing

Software
NameVersionClassification
PHENIX1.13rc2_2975refinement
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLP

1ylp


Resolution: 1.15→35.946 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.77 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 13912 5.01 %
Rwork0.1411 263588 -
obs0.1424 277500 89.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.58 Å2 / Biso mean: 12.6974 Å2 / Biso min: 3.57 Å2
Refinement stepCycle: final / Resolution: 1.15→35.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 138 890 4938
Biso mean--16.11 26.9 -
Num. residues----524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16310.26524500.24068207865784
1.1631-1.17680.24034070.23438310871784
1.1768-1.19110.22334110.21628356876785
1.1911-1.20620.2214180.21398325874385
1.2062-1.22210.24033870.2068509889685
1.2221-1.23880.21134220.19988363878586
1.2388-1.25650.22764710.19568396886786
1.2565-1.27530.21444100.198465887586
1.2753-1.29520.21853900.18358617900787
1.2952-1.31640.18914540.17788469892386
1.3164-1.33910.18334900.17098490898087
1.3391-1.36350.19134940.17068684917887
1.3635-1.38970.19474210.15928535895688
1.3897-1.41810.17874970.15198646914388
1.4181-1.44890.18954070.14378837924489
1.4489-1.48260.17174480.1398596904489
1.4826-1.51970.174950.13318745924089
1.5197-1.56080.15484720.12648840931290
1.5608-1.60670.16774840.12868891937590
1.6067-1.65860.15494740.12478881935591
1.6586-1.71780.16024560.12818984944091
1.7178-1.78660.16274540.13499002945692
1.7866-1.86790.1645010.12489051955292
1.8679-1.96640.15945100.129100961093
1.9664-2.08960.13654680.11859229969793
2.0896-2.25090.14384740.12089309978394
2.2509-2.47740.14995720.12799211978395
2.4774-2.83570.15455030.12929440994396
2.8357-3.57220.14525400.118894741001497
3.5722-35.96310.14435320.126296261015898

+
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