[English] 日本語
Yorodumi
- PDB-6q5b: OXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated cefta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q5b
TitleOXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated ceftazidime-avibactam resistance
Components(Beta-lactamase) x 2
KeywordsANTIBIOTIC / OXA-48 / ceftazidime / avibactam / resistance development / evolution / Escherichia coli / Klebsiella pneumoniae / carbapenemase / carbapenem
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBON DIOXIDE / Chem-NXL / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsFrohlich, C. / Sorum, V. / Thomassen, A.M. / Johnsen, P.J. / Leiros, H.K.S. / Samuelsen, O.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of NorwayA32689 Norway
CitationJournal: Msphere / Year: 2019
Title: OXA-48-Mediated Ceftazidime-Avibactam Resistance Is Associated with Evolutionary Trade-Offs.
Authors: Frohlich, C. / Sorum, V. / Thomassen, A.M. / Johnsen, P.J. / Leiros, H.S. / Samuelsen, O.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 8, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
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)122,96415
Polymers121,5694
Non-polymers1,39511
Water12,592699
1
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4698
Polymers60,7842
Non-polymers6856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-19 kcal/mol
Surface area20310 Å2
MethodPISA
2
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4947
Polymers60,7842
Non-polymers7105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-26 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.115, 105.802, 125.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Beta-lactamase


Mass: 30370.686 Da / Num. of mol.: 2 / Mutation: P68A
Source method: isolated from a genetically manipulated source
Details: A P68A mutatnt / Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3727643_05844, SAMEA3729690_05506
Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Protein Beta-lactamase


Mass: 30413.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3727643_05844, SAMEA3729690_05506
Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase

-
Non-polymers , 5 types, 710 molecules

#3: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic*YM
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 to 30 % polyethylene glycol monomethyl ether 5,000 and 0.1 M bis-tris propane buffer pH 6.5 to 7.5
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.22→25 Å / Num. obs: 58434 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.22 % / CC1/2: 0.994 / Rmerge(I) obs: 0.196 / Net I/σ(I): 6.8
Reflection shellResolution: 2.22→2.28 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5QB4

5qb4


Resolution: 2.22→24.831 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 2188 3.76 %
Rwork0.204 --
obs0.2062 58236 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→24.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7758 0 83 699 8540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128053
X-RAY DIFFRACTIONf_angle_d1.1810889
X-RAY DIFFRACTIONf_dihedral_angle_d21.5514725
X-RAY DIFFRACTIONf_chiral_restr0.061144
X-RAY DIFFRACTIONf_plane_restr0.0071396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.26830.35571100.26793476X-RAY DIFFRACTION100
2.2683-2.3210.32471590.27323445X-RAY DIFFRACTION100
2.321-2.3790.32131450.26083428X-RAY DIFFRACTION100
2.379-2.44330.29391240.25263473X-RAY DIFFRACTION100
2.4433-2.51510.32291260.24393499X-RAY DIFFRACTION100
2.5151-2.59620.32751230.24183470X-RAY DIFFRACTION100
2.5962-2.68890.3021460.23163447X-RAY DIFFRACTION100
2.6889-2.79640.28591510.21453475X-RAY DIFFRACTION100
2.7964-2.92350.29551420.21663482X-RAY DIFFRACTION100
2.9235-3.07730.26111280.21213491X-RAY DIFFRACTION100
3.0773-3.26980.27581350.20713538X-RAY DIFFRACTION100
3.2698-3.52160.24941490.18843474X-RAY DIFFRACTION99
3.5216-3.87480.24311340.16593525X-RAY DIFFRACTION100
3.8748-4.43270.20921490.1573558X-RAY DIFFRACTION100
4.4327-5.57430.18631410.16013556X-RAY DIFFRACTION99
5.5743-24.83260.27851260.2193711X-RAY DIFFRACTION99

+
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