[English] 日本語
Yorodumi
- PDB-2y90: Crystal structure of Hfq riboregulator from E. coli (P6 space group) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y90
TitleCrystal structure of Hfq riboregulator from E. coli (P6 space group)
ComponentsPROTEIN HFQ
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / SM-LIKE / RNA CHAPERONE
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / regulation of DNA-templated transcription / DNA binding / RNA 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: 2.252 Å
AuthorsBasquin, J. / Sauter, C.
Citation
Journal: Cryst. Growth Des. / Year: 2011
Title: Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination
Authors: Bonnefond, L. / Schellenberger, P. / Basquin, J. / Demangeat, G. / Ritzenthaler, C. / Chenevert, R. / Balg, C. / Frugier, M. / Rudinger-Thirion, J. / Giege, R. / Lorber, L. / Sauter, C.
#1: Journal: Nucleic Acids Res. / Year: 2003
Title: Sm-Like Proteins in Eubacteria: The Crystal Structure of the Hfq Protein from Escherichia Coli.
Authors: Sauter, C. / Basquin, J. / Suck, D.
History
DepositionFeb 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN HFQ


Theoretical massNumber of molelcules
Total (without water)11,3071
Polymers11,3071
Non-polymers00
Water19811
1
A: PROTEIN HFQ
x 6


Theoretical massNumber of molelcules
Total (without water)67,8456
Polymers67,8456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555y,-x+y,z1
Buried area8520 Å2
ΔGint-71.1 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.500, 61.500, 28.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein PROTEIN HFQ / HF-1 / HOST FACTOR-I PROTEIN / HF-I


Mass: 11307.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: P0A6X3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTWO AMINO ACIDS ADDED IN N-TERMINUS AND PROBABLE PROTEOLYTIC DEGRADATION AFTER RESIDUE 69. RESIDUES ...TWO AMINO ACIDS ADDED IN N-TERMINUS AND PROBABLE PROTEOLYTIC DEGRADATION AFTER RESIDUE 69. RESIDUES 70-102 ARE EITHER DISORDERED IN THE CRYSTAL OR ABSENT DUE TO PROTEOLYSIS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.7 Å3/Da / Density % sol: 30 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL HANGING DROPS AT 20C. THE RESERVOIR CONTAINED 1.6 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 8.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.313
ReflectionResolution: 2.25→54 Å / Num. obs: 2979 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 2.25→2.3 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.3 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 2.252→53.261 Å / σ(F): 0 / Phase error: 32.43 / Stereochemistry target values: TWIN_LSQ_F
Details: THE FULL LENGTH HFQ PROTEIN CRYSTALLIZED AFTER PROTEOLYTIC DEGRADATION AS INDICATED BY THE CRYSTAL SOLVENT SOLVENT CONTENT (SEE REF1). THE RESULTING MONOMER LACKS RESIDUES 70-102. THE LATTER ...Details: THE FULL LENGTH HFQ PROTEIN CRYSTALLIZED AFTER PROTEOLYTIC DEGRADATION AS INDICATED BY THE CRYSTAL SOLVENT SOLVENT CONTENT (SEE REF1). THE RESULTING MONOMER LACKS RESIDUES 70-102. THE LATTER ARE EITHER DISORDERED IN THE CRYSTAL OR ABSENT DUE TO BY PROTEOLYSIS.
RfactorNum. reflection% reflection
Rfree0.2258 232 7.8 %
Rwork0.1798 --
obs0.1881 2979 99.04 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.035 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.664 Å2-0 Å20 Å2
2---2.664 Å20 Å2
3---5.3279 Å2
Refinement stepCycle: LAST / Resolution: 2.252→53.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms510 0 0 11 521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007519
X-RAY DIFFRACTIONf_angle_d1.164704
X-RAY DIFFRACTIONf_dihedral_angle_d14.25197
X-RAY DIFFRACTIONf_chiral_restr0.07785
X-RAY DIFFRACTIONf_plane_restr0.00589
LS refinement shellResolution: 2.2608→24.9582 Å
RfactorNum. reflection% reflection
Rfree0.2262 232 -
Rwork0.1832 2713 -
obs--91 %

+
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