[English] 日本語
Yorodumi
- PDB-1dd5: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dd5
TitleCRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, RRF
ComponentsRIBOSOME RECYCLING FACTOR
KeywordsRIBOSOME / THREE-HELIX BUNDLE / BETA-ALPHA-BETA SANDWICH
Function / homology
Function and homology information


ribosomal large subunit binding / translational termination / translation / cytoplasm
Similarity search - Function
Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle ...Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Ribosome-recycling factor
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsSelmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A.
Citation
Journal: Science / Year: 1999
Title: Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic.
Authors: Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Analysis of Thermotoga Maritima Ribosome Recycling Factor
Authors: Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A.
#2: Journal: To be Published
Title: Cloning and Overexpression of Thermotoga Maritima RRF
Authors: Atarashi, K. / Kaji, A.
History
DepositionNov 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBOSOME RECYCLING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6683
Polymers21,5481
Non-polymers1202
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.250, 47.250, 297.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

-
Components

#1: Protein RIBOSOME RECYCLING FACTOR


Mass: 21548.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9X1B9
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: ammonium sulfate, acetate, glycerol , pH 5.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNH4Cl
40.5 mMdithiothreitol1drop
50.1 Msodium acetate1reservoir
62.0 Mammonium sulfate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONESRF BM1410.9786,0.9788,0.9184
SYNCHROTRONMAX II I71120.947
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMar 27, 1999
MARRESEARCH2IMAGE PLATEJan 13, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97881
30.91841
40.9471
ReflectionResolution: 2.55→30 Å / Num. all: 11927 / Num. obs: 11648 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 27
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1261 / % possible all: 91.8
Reflection shell
*PLUS
% possible obs: 91.8 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.55→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 1478170 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Solved by selenomethionine MAD
RfactorNum. reflection% reflectionSelection details
Rfree0.277 597 5 %RANDOM
Rwork0.23 ---
all0.232 11878 --
obs0.232 11878 99.3 %-
Solvent computationSolvent model: flat model / Bsol: 23.6 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 0 73 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it3.820.75
X-RAY DIFFRACTIONc_mcangle_it5.361
X-RAY DIFFRACTIONc_scbond_it11.212
X-RAY DIFFRACTIONc_scangle_it13.182.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 100 5.2 %
Rwork0.345 1808 -
obs--99.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

+
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