[English] 日本語
Yorodumi
- PDB-6fj1: Structure of the Ldtfm-avibactam carbamoyl enzyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fj1
TitleStructure of the Ldtfm-avibactam carbamoyl enzyme
ComponentsL,D-TRANSPEPTIDASE
KeywordsHYDROLASE / L / D-TRANSPEPTIDATION / PEPTIDOGLYCAN / ANTIBIOTIC RESISTANCE / AVIBACTAM / NXL104 / ANTIBIOTIC
Function / homology
Function and homology information


Ubiquitin-like (UB roll) - #800 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-NXL / 3,6,9,12,15-PENTAOXAHEPTADECANE / :
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLi de la Sierra Gallay, I. / Iannazzo, L. / Compain, F. / Fonvielle, M. / van Tilbeurgh, H. / Edoo, Z. / Arthur, M. / Etheve-Quelquejeu, M. / Hugonnet, J.
Funding support France, 2items
OrganizationGrant numberCountry
Fondation pour la recherche medicaleECO20160736080 France
French National Research AgencyANR-17-CE18-0010-03 France
CitationJournal: Chemistry / Year: 2018
Title: Synthesis of Avibactam Derivatives and Activity on beta-Lactamases and Peptidoglycan Biosynthesis Enzymes of Mycobacteria.
Authors: Edoo, Z. / Iannazzo, L. / Compain, F. / Li de la Sierra Gallay, I. / van Tilbeurgh, H. / Fonvielle, M. / Bouchet, F. / Le Run, E. / Mainardi, J.L. / Arthur, M. / Etheve-Quelquejeu, M. / Hugonnet, J.E.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L,D-TRANSPEPTIDASE
B: L,D-TRANSPEPTIDASE
C: L,D-TRANSPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,75518
Polymers86,4303
Non-polymers2,32515
Water1,820101
1
A: L,D-TRANSPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5476
Polymers28,8101
Non-polymers7375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-TRANSPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6967
Polymers28,8101
Non-polymers8866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: L,D-TRANSPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5125
Polymers28,8101
Non-polymers7024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.540, 131.970, 70.090
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 217 - 469 / Label seq-ID: 1 - 253

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein L,D-TRANSPEPTIDASE


Mass: 28809.910 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: CQR42_01530 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D0BNR1

-
Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O5
#3: 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.: 3 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 5.58 Å3/Da / Density % sol: 77.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Potassium nitrate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.69→48.04 Å / Num. obs: 52058 / % possible obs: 99 % / Redundancy: 3.41 % / Biso Wilson estimate: 70 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.13 / Net I/σ(I): 7.62
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 3.39 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 8090 / CC1/2: 0.72 / Rrim(I) all: 1.24 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZAT

1zat


Resolution: 2.69→48.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.419 / SU ML: 0.21 / SU R Cruickshank DPI: 0.2614 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.222
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2602 5 %RANDOM
Rwork0.1971 ---
obs0.1987 49437 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 251.55 Å2 / Biso mean: 83.319 Å2 / Biso min: 41.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å20.12 Å2
2--3.13 Å2-0 Å2
3----7 Å2
Refinement stepCycle: final / Resolution: 2.69→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 151 101 6192
Biso mean--129.49 60.93 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026238
X-RAY DIFFRACTIONr_bond_other_d0.0020.025544
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.968476
X-RAY DIFFRACTIONr_angle_other_deg1.075312970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45325.618267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29815984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.921512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216813
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021176
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161480.04
12B161480.04
21A160260.05
22C160260.05
31B160500.05
32C160500.05
LS refinement shellResolution: 2.692→2.762 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.546 175 -
Rwork0.526 3333 -
all-3508 -
obs--91.78 %

+
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