[English] 日本語
Yorodumi
- PDB-6ki9: Apo structure of FabMG, novel types of Enoyl-acyl carrier protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ki9
TitleApo structure of FabMG, novel types of Enoyl-acyl carrier protein reductase
ComponentsFabMG, novel types of Enoyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / Enoyl-acyl carrier protein reductase / FabMG
Function / homologySIR2_2 domain-containing protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsKim, S. / Rhee, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01325801 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1A2B4002860 Korea, Republic Of
CitationJournal: Febs J. / Year: 2020
Title: A triclosan-resistance protein from the soil metagenome is a novel enoyl-acyl carrier protein reductase: Structure-guided functional analysis.
Authors: Kim, S.H. / Khan, R. / Choi, K. / Lee, S.W. / Rhee, S.
History
DepositionJul 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FabMG, novel types of Enoyl-acyl carrier protein reductase
B: FabMG, novel types of Enoyl-acyl carrier protein reductase
C: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,77523
Polymers148,2703
Non-polymers1,50620
Water16,538918
1
A: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,11410
Polymers49,4231
Non-polymers6919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9908
Polymers49,4231
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FabMG, novel types of Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6725
Polymers49,4231
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.862, 137.005, 156.862
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARGchain 'A'AA1 - 561 - 56
12ASNASNGLUGLUchain 'A'AA60 - 44060 - 440
23METMETARGARGchain 'B'BB1 - 561 - 56
24ASNASNGLUGLUchain 'B'BB60 - 44060 - 440

-
Components

#1: Protein FabMG, novel types of Enoyl-acyl carrier protein reductase


Mass: 49423.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1C9HA64
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 918 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-tris (pH 6.5), 23% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 168488 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 22.0727481816 Å2 / CC1/2: 0.999 / Net I/σ(I): 32.8
Reflection shellResolution: 1.644→1.703 Å / Num. unique obs: 16628 / CC1/2: 0.841

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→26.7277265571 Å / SU ML: 0.174965452937 / Cross valid method: NONE / σ(F): 1.33792973872 / Phase error: 25.740589025
RfactorNum. reflection% reflection
Rfree0.241672819757 2000 1.18795179292 %
Rwork0.216979745648 --
obs0.217272860095 168357 99.9246219226 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.6359567753 Å2
Refinement stepCycle: LAST / Resolution: 1.64→26.7277265571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9587 0 98 918 10603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004504849057999858
X-RAY DIFFRACTIONf_angle_d0.8736121387513280
X-RAY DIFFRACTIONf_chiral_restr0.03374288337151468
X-RAY DIFFRACTIONf_plane_restr0.004669911971981703
X-RAY DIFFRACTIONf_dihedral_angle_d12.40021538593607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.68170.3206280618141410.28596916802411754X-RAY DIFFRACTION99.848904558
1.6817-1.72710.284821874681420.27350539080611765X-RAY DIFFRACTION99.9580255205
1.7271-1.77790.3375980290331410.27807774091511776X-RAY DIFFRACTION99.9496770947
1.7779-1.83530.2683907211131420.26118406366211732X-RAY DIFFRACTION99.9494949495
1.8353-1.90090.2714176423021410.25778022699711785X-RAY DIFFRACTION99.974851203
1.9009-1.9770.2868426703291420.25226398901311818X-RAY DIFFRACTION99.991639495
1.977-2.06690.2700985286251430.24174052896611862X-RAY DIFFRACTION99.9916708313
2.0669-2.17580.283679012491420.22885527401211824X-RAY DIFFRACTION100
2.1758-2.31210.2505081652241430.23155720752511847X-RAY DIFFRACTION99.991660412
2.3121-2.49050.2630240436931420.22966258811871X-RAY DIFFRACTION100
2.4905-2.74090.2467617517281440.22451214081111937X-RAY DIFFRACTION99.9917232246
2.7409-3.1370.2714360842051430.22144876045311957X-RAY DIFFRACTION99.983473806
3.137-3.95020.1988239420691450.19210843065612070X-RAY DIFFRACTION99.9918140144
3.9502-26.7270.2018091493691490.18096159926112359X-RAY DIFFRACTION99.3486894361
Refinement TLS params.Method: refined / Origin x: -15.0214671035 Å / Origin y: 21.2549402238 Å / Origin z: 32.0679171839 Å
111213212223313233
T0.150990816777 Å20.00513040573484 Å20.00319246288151 Å2-0.162331556815 Å20.0516506590137 Å2--0.240014270466 Å2
L0.0574361386837 °20.0546377795978 °2-0.0351505485932 °2-0.113321388837 °2-0.146351156737 °2--0.34338646088 °2
S0.00624738891465 Å °-0.0280643155341 Å °-0.0297520082378 Å °0.0854838496624 Å °0.0157575384023 Å °-0.00833413707392 Å °-0.00958346178226 Å °-0.0260695183182 Å °-0.0253256024526 Å °
Refinement TLS groupSelection details: all

+
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