[English] 日本語
Yorodumi
- PDB-3qhs: Crystal structure of full-length Hfq from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qhs
TitleCrystal structure of full-length Hfq from Escherichia coli
ComponentsProtein hfq
KeywordsRNA BINDING PROTEIN / SM-LIKE / PLEIOTROPIC REGULATOR
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / bacterial nucleoid / regulation of translation, ncRNA-mediated / bent DNA binding / regulation of RNA stability / RNA folding chaperone / tRNA processing / tRNA binding / regulation of DNA-templated transcription / DNA binding / RNA binding / ATP binding / cytosol
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBeich-Frandsen, M. / Vecerek, B. / Sjoeblom, B. / Blaesi, U. / Djinovic-Carugo, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structural analysis of full-length Hfq from Escherichia coli
Authors: Beich-Frandsen, M. / Vecerek, B. / Sjoblom, B. / Blasi, U. / Djinovic-Carugo, K.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Protein hfq
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq
G: Protein hfq
H: Protein hfq
I: Protein hfq
J: Protein hfq
K: Protein hfq
L: Protein hfq


Theoretical massNumber of molelcules
Total (without water)134,15212
Polymers134,15212
Non-polymers00
Water1,27971
1
A: Protein hfq
B: Protein hfq
C: Protein hfq
D: Protein hfq
E: Protein hfq
F: Protein hfq


Theoretical massNumber of molelcules
Total (without water)67,0766
Polymers67,0766
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-71 kcal/mol
Surface area18890 Å2
MethodPISA
2
G: Protein hfq
H: Protein hfq
I: Protein hfq
J: Protein hfq
K: Protein hfq
L: Protein hfq


Theoretical massNumber of molelcules
Total (without water)67,0766
Polymers67,0766
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-70 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.910, 62.150, 81.260
Angle α, β, γ (deg.)78.56, 86.16, 59.86
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Protein hfq / HF-1 / Host factor-I protein / HF-I


Mass: 11179.354 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4172, hfq, JW4130 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6X3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% v/v PEG 550 MME, 0.05M calcium chloride dihydrate, 0.1M BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.933 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.85→80 Å / Num. all: 23985 / Num. obs: 23973 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.03 % / Biso Wilson estimate: 25.33 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 14.22
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 6.43 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.6 / Num. unique all: 9573 / % possible all: 83.7

-
Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 2.85→45.214 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.483 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24969 1197 5.1 %RANDOM
Rwork0.20694 ---
all0.20919 22301 --
obs0.20919 22301 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.979 Å2
Baniso -1Baniso -2Baniso -3
1--6.77 Å22.88 Å20.92 Å2
2---4.64 Å2-2.12 Å2
3---9.24 Å2
Refinement stepCycle: LAST / Resolution: 2.85→45.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 0 71 6563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226623
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.9578985
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2315800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8123.547296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.496151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6961548
X-RAY DIFFRACTIONr_chiral_restr0.080.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6871.54071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.30126690
X-RAY DIFFRACTIONr_scbond_it2.34332552
X-RAY DIFFRACTIONr_scangle_it3.7324.52295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 83
Rwork0.281 1656

+
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