[English] 日本語
Yorodumi
- PDB-8cum: X-ray crystal structure of OXA-24/40 in complex with sulfonamidob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cum
TitleX-ray crystal structure of OXA-24/40 in complex with sulfonamidoboronic acid 6d
ComponentsBeta-lactamase
KeywordsHYDROLASE/Inhibitor / Carbapenemase / Inhibitor / BATSI / HYDROLASE / HYDROLASE-Inhibitor complex
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / beta-lactamase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / Chem-OZ0 / Beta-lactamase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsFernando, M.C. / Wallar, B.J. / Powers, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: Antibiotics / Year: 2023
Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat ...Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii .
Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / ...Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / Hujer, A.M. / Prati, F. / Powers, R.A. / Bonomo, R.A. / Caselli, E.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5958
Polymers27,7181
Non-polymers8787
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Monomeric biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.190, 102.190, 85.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-626-

HOH

-
Components

#1: Protein Beta-lactamase / / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 ...Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing class D beta-lactamase OXA-24 / Carbapenem-hydrolyzing oxacillinase / Carbapenem-hydrolyzing oxacillinase OXA-40 / Carbapenemase OXA-24 / Class D beta-lactamase OXA-40 / OXA-24 class D beta-lactamase / OXA24 B-lactamase / Oxa40


Mass: 27717.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RLA6, beta-lactamase
#2: Chemical ChemComp-OZ0 / 3-({[(1S)-1-boronopropyl]sulfamoyl}methyl)benzoic acid


Mass: 301.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16BNO6S / Feature type: SUBJECT OF INVESTIGATION
#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.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium pH 7.5 2% PEG 400 2.0 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.49→55.26 Å / Num. obs: 74330 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 19.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.035 / Rrim(I) all: 0.099 / Net I/σ(I): 12.6 / Num. measured all: 597202
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.49-1.537.92.2514230653890.4190.8462.4070.999.2
6.66-55.266.80.02965059620.9990.0110.0314199.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAE

3pae


Resolution: 1.49→51.09 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 3689 4.97 %
Rwork0.1893 70570 -
obs0.1903 74259 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.21 Å2 / Biso mean: 25.99 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 1.49→51.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 64 287 2278
Biso mean--32.74 37.18 -
Num. residues----244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.510.43111370.40852640277798
1.51-1.530.43171300.37462682281299
1.53-1.550.36491410.358726722813100
1.55-1.580.31171210.31612690281199
1.58-1.60.30691520.309326562808100
1.6-1.630.29991440.276526712815100
1.63-1.650.30861130.270626962809100
1.65-1.680.27041470.25826732820100
1.68-1.720.24811470.246326662813100
1.72-1.750.22671390.242427062845100
1.75-1.790.25391380.227126862824100
1.79-1.830.28031380.235426922830100
1.83-1.880.27311520.216326942846100
1.88-1.930.22421370.199127082845100
1.93-1.980.19731430.190526822825100
1.98-2.050.20991450.183327222867100
2.05-2.120.21591390.173227072846100
2.12-2.210.18931360.17826982834100
2.21-2.310.21371340.179727462880100
2.31-2.430.18251530.174927152868100
2.43-2.580.20291350.178727382873100
2.58-2.780.20751720.181627292901100
2.78-3.060.20751320.181127612893100
3.06-3.50.17051530.160127852938100
3.5-4.410.1521570.138727882945100
4.41-51.090.19961540.183329673121100

+
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