[English] 日本語
Yorodumi
- PDB-1u1t: Hfq protein from Pseudomonas aeruginosa. High-salt crystals -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u1t
TitleHfq protein from Pseudomonas aeruginosa. High-salt crystals
ComponentsHfq protein
KeywordsRNA BINDING PROTEIN / Hfq / HF1 / Sm-like bacterial protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


regulation of carbon utilization / regulation of translation, ncRNA-mediated / regulation of RNA stability / quorum sensing / regulation of translation / regulation of DNA-templated transcription / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNikulin, A.D. / Stolboushkina, E.A. / Perederina, A.A. / Vassilieva, I.M. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. ...Nikulin, A.D. / Stolboushkina, E.A. / Perederina, A.A. / Vassilieva, I.M. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S.V. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Pseudomonas aeruginosa Hfq protein.
Authors: Nikulin, A. / Stolboushkina, E. / Perederina, A. / Vassilieva, I. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S.
History
DepositionJul 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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: Hfq protein
B: Hfq protein
C: Hfq protein
D: Hfq protein
E: Hfq protein
F: Hfq protein


Theoretical massNumber of molelcules
Total (without water)54,6876
Polymers54,6876
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-77 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 72.350, 109.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Hfq protein /


Mass: 9114.487 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hfq / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9HUM0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 M Li2SO4, 0.6 M ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Type: SPRING-8 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 40524 / Num. obs: 40524 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.8 / Num. unique all: 9200 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HK9

1hk9


Resolution: 1.9→24.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3567365.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1878 4.9 %RANDOM
Rwork0.205 ---
all0.222 39911 --
obs0.205 38033 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1183 Å2 / ksol: 0.371734 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.24 Å20 Å20 Å2
2--1.79 Å20 Å2
3---8.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 164 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.341.5
X-RAY DIFFRACTIONc_mcangle_it6.42
X-RAY DIFFRACTIONc_scbond_it7.072
X-RAY DIFFRACTIONc_scangle_it9.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 315 5.1 %
Rwork0.329 5817 -
obs-5817 95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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