[English] 日本語
Yorodumi
- PDB-2ylb: Structure of Salmonella typhimurium Hfq at 1.15 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ylb
TitleStructure of Salmonella typhimurium Hfq at 1.15 A
ComponentsPROTEIN HFQ
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / LSM PROTEIN / RNA CHAPERONE
Function / homology
Function and homology information


regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / RNA binding / identical protein 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 speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsSauer, E. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural Basis for RNA 3' End Recognition by Hfq
Authors: Sauer, E. / Weichenrieder, O.
History
DepositionJun 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Atomic model / Other
Revision 1.2Aug 24, 2011Group: Database references
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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 30-STRANDED BARREL THIS IS REPRESENTED BY A 31-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
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


Theoretical massNumber of molelcules
Total (without water)49,5456
Polymers49,5456
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-73.5 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.400, 61.400, 167.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

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


Mass: 8257.572 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-72
Source method: isolated from a genetically manipulated source
Details: THE SEQUENCE IS PRECEDED BY A GA TAG REMAINING FROM THE PURIFICATION TAG.
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: LT2 / Plasmid: PET M60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: P0A1R0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS PRECEDED BY A GA TAG REMAINING FROM THE PURIFICATION TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES (PH=7.0), 0.5 % JEFFAMINE, 1.1 M MALONATE

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.827
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. obs: 123284 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 8.2 Å2 / Rsym value: 0.067 / Net I/σ(I): 12.8
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.52 / Rsym value: 0.64 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 1.15→18.84 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 21.88 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. B FACTORS WERE REFINED ANISOTROPICALLY FOR NON-HYDROGEN ATOMS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUES ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. B FACTORS WERE REFINED ANISOTROPICALLY FOR NON-HYDROGEN ATOMS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUES 60, 66. CHAIN B, RESIDUES 17, 19, 36, 38, 60, 66. CHAIN C, RESIDUES 17, 38, 60, 61, 66. CHAIN D, RESIDUES 13, 36. CHAIN E, RESIDUES 36, 66. CHAIN F, RESIDUE 61.THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1 TO 5, 71 TO 72. CHAIN B, RESIDUES 1 TO 6, 72. CHAIN C, RESIDUES 1 TO 3, 72. CHAIN D, RESIDUES 1 TO 3, 72. CHAIN E, RESIDUES 1 TO 3, 72. CHAIN F, RESIDUES 1 TO 5, 72.
RfactorNum. reflection% reflection
Rfree0.2076 6171 5 %
Rwork0.1682 --
obs0.1701 123284 98 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.557 Å2 / ksol: 0.461 e/Å3
Displacement parametersBiso mean: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.3713 Å20 Å20 Å2
2--0.3713 Å20 Å2
3----0.7426 Å2
Refinement stepCycle: LAST / Resolution: 1.15→18.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 0 376 3579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153423
X-RAY DIFFRACTIONf_angle_d1.6144665
X-RAY DIFFRACTIONf_dihedral_angle_d13.2381313
X-RAY DIFFRACTIONf_chiral_restr0.093546
X-RAY DIFFRACTIONf_plane_restr0.008602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.19110.29725770.244611634X-RAY DIFFRACTION97
1.1911-1.23880.27536420.231111717X-RAY DIFFRACTION98
1.2388-1.29520.25496220.210411826X-RAY DIFFRACTION99
1.2952-1.36340.24726390.191811847X-RAY DIFFRACTION99
1.3634-1.44880.22626360.17411760X-RAY DIFFRACTION99
1.4488-1.56060.20476300.155911819X-RAY DIFFRACTION99
1.5606-1.71760.19986250.144511725X-RAY DIFFRACTION98
1.7176-1.96590.17346250.13711735X-RAY DIFFRACTION98
1.9659-2.47590.16595690.137311668X-RAY DIFFRACTION97
2.4759-18.84250.20286060.172211382X-RAY DIFFRACTION95

+
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