[English] 日本語
Yorodumi
- PDB-6bdg: HFQ monomer in spacegroup p6 at 1.93 angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bdg
TitleHFQ monomer in spacegroup p6 at 1.93 angstrom resolution
ComponentsRNA-binding protein Hfq
KeywordsCHAPERONE / RNA binding chaperone
Function / homology
Function and homology information


regulation of DNA-templated transcription / RNA binding
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA-binding protein Hfq
Similarity search - Component
Biological speciesEscherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.964 Å
AuthorsBrown, C. / Zhang, K. / Seo, C. / Ellis, M.J. / Hanniford, D.B. / Junop, M.
CitationJournal: To Be Published
Title: HFQ monomer in spacegroup p6 at 1.93 angstrom resolution
Authors: Ellis, M.J. / Brown, C. / Zhang, K. / Seo, C. / Junop, M. / Hanniford, D.B.
History
DepositionOct 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA-binding protein Hfq


Theoretical massNumber of molelcules
Total (without water)7,3011
Polymers7,3011
Non-polymers00
Water73941
1
A: RNA-binding protein Hfq
x 6


Theoretical massNumber of molelcules
Total (without water)43,8036
Polymers43,8036
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area8530 Å2
ΔGint-73 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.370, 61.370, 28.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein RNA-binding protein Hfq


Mass: 7300.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: hfq, ECS88_4758 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MKX6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na/K phosphate pH 6.2 10 % W/V PEG 3000 10 mM Spermidine 5 mM Mg Acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→19.36 Å / Num. obs: 4191 / % possible obs: 94 % / Redundancy: 2 % / CC1/2: 0.991 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9644→2.2483 Å / Redundancy: 1.9 % / CC1/2: 0.862 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.964→19.359 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2327 424 10.12 %
Rwork0.1917 --
obs0.1961 4189 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.964→19.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 0 41 555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007524
X-RAY DIFFRACTIONf_angle_d1.065711
X-RAY DIFFRACTIONf_dihedral_angle_d13.982198
X-RAY DIFFRACTIONf_chiral_restr0.03885
X-RAY DIFFRACTIONf_plane_restr0.00690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9644-2.24830.24741350.20731239X-RAY DIFFRACTION94
2.2483-2.83130.27641350.21481221X-RAY DIFFRACTION97
2.8313-19.36020.20721540.17481305X-RAY DIFFRACTION96

+
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