[English] 日本語
Yorodumi
- PDB-4k59: Crystal Structure of Pseudomonas Aeruginosa RsmF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k59
TitleCrystal Structure of Pseudomonas Aeruginosa RsmF
ComponentsRNA BINDING PROTEIN RsmF
KeywordsRNA BINDING PROTEIN / beta sandwich
Function / homology
Function and homology information


regulation of carbohydrate metabolic process / mRNA catabolic process / RNA binding / identical protein binding
Similarity search - Function
Translational regulator CsrA / Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carbon storage regulator / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsBetts, L. / Walton, W.G. / Redinbo, M.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: An unusual CsrA family member operates in series with RsmA to amplify posttranscriptional responses in Pseudomonas aeruginosa.
Authors: Marden, J.N. / Diaz, M.R. / Walton, W.G. / Gode, C.J. / Betts, L. / Urbanowski, M.L. / Redinbo, M.R. / Yahr, T.L. / Wolfgang, M.C.
History
DepositionApr 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA BINDING PROTEIN RsmF


Theoretical massNumber of molelcules
Total (without water)8,0671
Polymers8,0671
Non-polymers00
Water28816
1
A: RNA BINDING PROTEIN RsmF

A: RNA BINDING PROTEIN RsmF


Theoretical massNumber of molelcules
Total (without water)16,1352
Polymers16,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area2600 Å2
ΔGint-16 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.451, 41.451, 74.048
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

21A-113-

HOH

-
Components

#1: Protein RNA BINDING PROTEIN RsmF


Mass: 8067.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_68470 / Plasmid: pMCSG-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q02EI1, UniProt: A0A0H2ZIZ8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 4000, 0.2 M Magnesium chloride, 0.1 M Tris-HCl, pH 8.5, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2012 / Details: Confocal optics
RadiationMonochromator: Confocal optic / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 3743 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.83 Å2 / Rmerge(I) obs: 0.049 / Χ2: 1.468 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.22-2.262.80.3681700.665193.9
2.26-2.33.30.3521990.741197.5
2.3-2.343.60.3021720.8331100
2.34-2.393.90.2491860.881100
2.39-2.4440.2551910.8341100
2.44-2.54.10.2351820.861199.5
2.5-2.564.10.2121880.808199.5
2.56-2.6340.1631810.879199.5
2.63-2.714.10.1511811.001199.5
2.71-2.84.10.1321890.894199.5
2.8-2.94.10.1031791.029198.9
2.9-3.014.20.081961.1051100
3.01-3.154.20.0681911.203199.5
3.15-3.324.20.0531731.459199.4
3.32-3.5240.0491951.855199.5
3.52-3.84.10.0451902.025199.5
3.8-4.183.90.0381911.871198.5
4.18-4.7840.0291861.849197.9
4.78-6.0240.031951.749198.5
6.02-503.60.0392086.478196.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→32.302 Å / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.711 / SU ML: 0.27 / σ(F): 1.37 / Phase error: 34.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 358 9.62 %
Rwork0.2212 --
obs0.2257 3723 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.22 Å2 / Biso mean: 62.6779 Å2 / Biso min: 27.06 Å2
Refinement stepCycle: LAST / Resolution: 2.22→32.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 0 16 522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005509
X-RAY DIFFRACTIONf_angle_d1.022684
X-RAY DIFFRACTIONf_chiral_restr0.06782
X-RAY DIFFRACTIONf_plane_restr0.00389
X-RAY DIFFRACTIONf_dihedral_angle_d14.521199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.53930.30241140.24451100121498
2.5393-3.19880.35051230.262411141237100
3.1988-32.30540.23591210.20321151127299

+
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