[English] 日本語
Yorodumi
- PDB-6n9b: FtsY-NG ultra high-resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n9b
TitleFtsY-NG ultra high-resolution
ComponentsSignal recognition particle receptor FtsY
KeywordsTRANSPORT PROTEIN / FtsY / SRP / Signal recognition particle receptor / SR
Function / homology
Function and homology information


signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity ...signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain ...Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.219 Å
AuthorsAtaide, S.F. / Faoro, C.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural insights into the G-loop dynamics of E. coli FtsY NG domain.
Authors: Faoro, C. / Ataide, S.F.
History
DepositionDec 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal recognition particle receptor FtsY
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3204
Polymers66,2022
Non-polymers1182
Water14,574809
1
A: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1602
Polymers33,1011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle receptor FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1602
Polymers33,1011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.683, 76.180, 108.786
Angle α, β, γ (deg.)90.00, 93.87, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Signal recognition particle receptor FtsY / SRP receptor


Mass: 33101.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ftsY, b3464, JW3429
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10121
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.6, 24% PEG 2000 MME, 200 mM KBr.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.219→44.2 Å / Num. obs: 165619 / % possible obs: 98.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 14.75
Reflection shellResolution: 1.219→1.263 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQP

6cqp


Resolution: 1.219→44.2 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1788 8167 4.93 %
Rwork0.1552 --
obs0.1565 165612 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.219→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 8 809 5450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124741
X-RAY DIFFRACTIONf_angle_d1.1146386
X-RAY DIFFRACTIONf_dihedral_angle_d16.9421792
X-RAY DIFFRACTIONf_chiral_restr0.08748
X-RAY DIFFRACTIONf_plane_restr0.007831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2186-1.23250.34722660.31754913X-RAY DIFFRACTION92
1.2325-1.2470.28972700.26365141X-RAY DIFFRACTION97
1.247-1.26220.2982630.25545130X-RAY DIFFRACTION97
1.2622-1.27820.26112690.23465197X-RAY DIFFRACTION97
1.2782-1.2950.25962430.21535167X-RAY DIFFRACTION97
1.295-1.31270.24082720.19765199X-RAY DIFFRACTION98
1.3127-1.33150.21512830.19015224X-RAY DIFFRACTION98
1.3315-1.35130.21892500.17885174X-RAY DIFFRACTION98
1.3513-1.37250.20672650.17565179X-RAY DIFFRACTION98
1.3725-1.3950.22673160.17695226X-RAY DIFFRACTION98
1.395-1.4190.20042610.17025186X-RAY DIFFRACTION98
1.419-1.44480.21362720.17365277X-RAY DIFFRACTION99
1.4448-1.47260.19512760.16385157X-RAY DIFFRACTION98
1.4726-1.50270.19622670.15465265X-RAY DIFFRACTION99
1.5027-1.53530.19372630.13825219X-RAY DIFFRACTION99
1.5353-1.57110.1972480.13575310X-RAY DIFFRACTION99
1.5711-1.61040.17882710.13415254X-RAY DIFFRACTION99
1.6104-1.65390.16112300.13145357X-RAY DIFFRACTION99
1.6539-1.70260.17052560.13575242X-RAY DIFFRACTION99
1.7026-1.75750.15642700.14225304X-RAY DIFFRACTION99
1.7575-1.82030.18762500.14735361X-RAY DIFFRACTION99
1.8203-1.89320.17642850.15415237X-RAY DIFFRACTION100
1.8932-1.97940.183020.14925282X-RAY DIFFRACTION100
1.9794-2.08370.17912900.1495306X-RAY DIFFRACTION100
2.0837-2.21430.16472570.14315346X-RAY DIFFRACTION100
2.2143-2.38530.15962920.14015313X-RAY DIFFRACTION100
2.3853-2.62530.16653150.14945324X-RAY DIFFRACTION100
2.6253-3.00510.19772490.16025376X-RAY DIFFRACTION100
3.0051-3.78580.15933340.15155332X-RAY DIFFRACTION100
3.7858-44.22950.16352820.15355447X-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