[English] 日本語
Yorodumi
- PDB-1kkg: NMR Structure of Ribosome-Binding Factor A (RbfA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kkg
TitleNMR Structure of Ribosome-Binding Factor A (RbfA)
Componentsribosome-binding factor A
KeywordsSTRUCTURAL GENOMICS / cold-shock adaptation / ribosome-binding factor / NESG Project / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


ribosomal small subunit binding / response to cold / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / DNA damage response / cytosol
Similarity search - Function
Ribosome-binding factor A, conserved site / Ribosome-binding factor A signature. / Ribosome-binding factor A / Ribosome-binding factor A domain superfamily / Ribosome-binding factor A / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
30S ribosome-binding factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, automated analysis of NOESY data, 3D structures.
AuthorsHuang, Y.J. / Swapna, G.V.T. / Rajan, P.K. / Ke, H. / Xia, B. / Shukla, K. / Inouye, M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Solution NMR Structure of Ribosome-binding Factor A (RbfA), A Cold-shock Adaptation Protein from Escherichia coli
Authors: Huang, Y.J. / Swapna, G.V.T. / Rajan, P.K. / Ke, H. / Xia, B. / Shukla, K. / Inouye, M. / Montelione, G.T.
#1: Journal: J.BIOMOL.NMR / Year: 2001
Title: Resonance Assignments for Cold-shock Protein Ribosome-Binding Factor A (RbfA) from Escherichia coli.
Authors: Swapna, G.V. / Shukla, K. / Huang, Y.J. / Ke, H. / Xia, B. / Inouye, M. / Montelione, G.T.
History
DepositionDec 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ribosome-binding factor A


Theoretical massNumber of molelcules
Total (without water)12,2891
Polymers12,2891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 200Best target function
RepresentativeModel #1lowest value of target function

-
Components

#1: Protein ribosome-binding factor A / RBFA / COLD-SHOCK ADAPTATION PROTEIN


Mass: 12289.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rbfA / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A7G2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
132NH HSQC Jhahn
142NH HSQC 1H/2H exchange
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY, AUTOMATED ANALYSIS OF ASSIGNMENTS AND AUTOMATED ANALYSIS OF 3D STRUCTURE.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM RbfA, U-15N,13C; 10 mM sodium phosphate, 0.5 mM sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
21.6 mM RbfA, U-15N; 10 mM potassium acetate 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 10 mM / pH: 5.05 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
AutoAssign1.7.7Moseley, H., Zimmermann, D.E., Huang, Y.J., Kulikowski, C.G. and Montelione, G.T.data analysis
AutoStructure1.0alphaHuang, Y.J., Tejero, R. and Montelione, G.T.data analysis
Sparky3.69Goddard, T.D. and Kneller, D.G.data analysis
VNMR6.3bVarian Inc.processing
DYANA1.5Guntert, P., Mumenthaler, C. and Wuthrich, K.refinement
TALOS98.040.21.02Cornilescu, G., Delaglio, F. and Bax, A.data analysis
RefinementMethod: simulated annealing, torsion angle dynamics, automated analysis of NOESY data, 3D structures.
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1970 RESTRAINTS, 1698 CONFORMATIONALLY-RESTRICTING NOE- DERIVED DISTANCE CONSTRAINTS, 184 DIHEDRAL ANGLE CONSTRAINTS, 88 DISTANCE RESTRAINTS FROM ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1970 RESTRAINTS, 1698 CONFORMATIONALLY-RESTRICTING NOE- DERIVED DISTANCE CONSTRAINTS, 184 DIHEDRAL ANGLE CONSTRAINTS, 88 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. SUMMARY OF RBFA STRUCTURE CALCULATION BY AUTOSTRUCTURE: SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 1698; INTRA-RESIDUE [I=J] = 175; SEQUENTIAL [(I-J)=1] = 454; MEDIUM RANGE [1<(I-J)<5] = 595; LONG RANGE [(I-J)>=5] = 474; NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE = 15.7; DIHEDRAL-ANGLE CONSTRAINTS = 184; TOTAL HYDROGEN BOND CONSTRAINTS = 88; LONG RANGE HYDROGEN BOND CONSTRAINTS = 24; TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 18.2; NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 4.6; NUMBER OF STRUCTURES COMPUTED = 200; NUMBER OF STRUCTURES USED = 16. RESIDUAL CONSTRAINT VIOLATIONS: DISTANCE VIOLATIONS 0.1-0.2ANG = 31; 0.2-0.5ANG = 9; >0.5ANG = 1. MAX DISTANCE VIOLATION = 0.57ANG; AVERAGE DISTANCE VIOLATION = 0.00ANG. MAX. VDW VIOLATION = 0.37 ANG. DIHEDRAL ANGLE VIOLATIONS: 0 - 10 DEG = 6; >10 DEG = 0; MAX ANGLE VIOLATION = 9 DEG; AVERAGE ANGLE VIOLATION = 0.06 DEG. RMSD VALUES : ALL BACKBONE ATOMS OF ALL RESIDUES = 0.5 ANG; ALL BACKBONE ATOMS OF ORDERED RESIDUES = 0.5 ANG; ALL HEAVY ATOMS OF ALL RESIDUES = 1.0 ANG; ALL HEAVY ATOMS OF ORDERED RESIDUES = 1.0 ANG. PROCHECK USING ALL RESIDUES: MOST FAVORED REGIONS = 73%; ADDITIONAL ALLOWED REGIONS = 23%; GENEROUSLY ALLOWED REGIONS = 4%; DISALLOWED REGIONS = 0%. NMR R-FACTORS : M = 39% I=46% L=27% . SPECTRAL INFORMATION: TOTAL NUMBER OF PEAKS IN N15-NOESY = 1536; TOTAL NUMBER OF ASSIGNABLE PEAKS IN N15- NOESY = 1239; TOTAL NUMBER OF PEAKS ASSIGNED IN N15-NOESY = 814; TOTAL NUMBER OF PEAKS IN C13-NOESY = 3115; TOTAL NUMBER OF ASSIGNABLE PEAKS IN C13-NOESY = 2494; TOTAL NUMBER OF PEAKS ASSIGNED IN C13-NOESY = 1802.
NMR representativeSelection criteria: lowest value of target function
NMR ensembleConformer selection criteria: Best target function / Conformers calculated total number: 200 / Conformers submitted total number: 16

+
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