[English] 日本語
Yorodumi
- PDB-6d3g: PER-2 class A extended-spectrum beta-lactamase crystal structure ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d3g
TitlePER-2 class A extended-spectrum beta-lactamase crystal structure in complex with avibactam at 2.4 Angstrom resolution
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DBO / penicilloil-serine-transferase / antibiotic resistance / 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 class A, catalytic domain / 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-NXL / Beta-lactamase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsPower, P. / Ruggiero, M. / Gutkind, G. / Bonomo, R. / Klinke, S.
Funding support Argentina, 2items
OrganizationGrant numberCountry
ANPCYTPICT-2004-0457 Argentina
FONCYTPPL-2011-2-0003 Argentina
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Structural Insights into the Inhibition of the Extended-Spectrum beta-Lactamase PER-2 by Avibactam.
Authors: Ruggiero, M. / Papp-Wallace, K.M. / Brunetti, F. / Barnes, M.D. / Bonomo, R.A. / Gutkind, G. / Klinke, S. / Power, P.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0899
Polymers123,8254
Non-polymers1,2635
Water1,33374
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers30,9561
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4183
Polymers30,9561
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers30,9561
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2242
Polymers30,9561
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.160, 85.840, 161.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Beta-lactamase /


Mass: 30956.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: blaPER-2 / Plasmid: pET28/PER-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2RP81, beta-lactamase
#2: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 6000, 0.05 M imidazole pH=8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.398→48.17 Å / Num. obs: 46410 / % possible obs: 99.76 % / Redundancy: 6.65 % / Biso Wilson estimate: 55.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Net I/σ(I): 13.73
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 6.65 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 7289 / CC1/2: 0.746 / Rrim(I) all: 1 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIX1.12-2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2O

4d2o


Resolution: 2.398→48.17 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.31
RfactorNum. reflection% reflection
Rfree0.2525 2321 5 %
Rwork0.2059 --
obs0.2083 46400 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.73 Å2
Refinement stepCycle: LAST / Resolution: 2.398→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8546 0 81 74 8701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138791
X-RAY DIFFRACTIONf_angle_d1.55911934
X-RAY DIFFRACTIONf_dihedral_angle_d13.9725299
X-RAY DIFFRACTIONf_chiral_restr0.0951396
X-RAY DIFFRACTIONf_plane_restr0.0111528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.398-2.44690.35131290.29622450X-RAY DIFFRACTION97
2.4469-2.50010.34541350.27462558X-RAY DIFFRACTION100
2.5001-2.55830.36061360.2712586X-RAY DIFFRACTION100
2.5583-2.62230.30791340.25552551X-RAY DIFFRACTION100
2.6223-2.69320.31731350.24842564X-RAY DIFFRACTION100
2.6932-2.77240.29011360.25192575X-RAY DIFFRACTION100
2.7724-2.86190.37391350.26312568X-RAY DIFFRACTION100
2.8619-2.96420.32181360.27672579X-RAY DIFFRACTION100
2.9642-3.08280.33951360.27692583X-RAY DIFFRACTION100
3.0828-3.22310.30331350.25592565X-RAY DIFFRACTION100
3.2231-3.3930.32991360.23982586X-RAY DIFFRACTION100
3.393-3.60550.30841370.22152598X-RAY DIFFRACTION100
3.6055-3.88380.24531370.20292618X-RAY DIFFRACTION100
3.8838-4.27440.20081380.17162611X-RAY DIFFRACTION100
4.2744-4.89240.18521380.16192626X-RAY DIFFRACTION100
4.8924-6.16190.21111410.18362668X-RAY DIFFRACTION100
6.1619-48.180.19551470.16282793X-RAY DIFFRACTION100

+
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