[English] 日本語
Yorodumi
- PDB-2czj: Crystal structure of the tRNA domain of tmRNA from Thermus thermo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2czj
TitleCrystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8
Components
  • SsrA-binding protein
  • tmRNA (63-MER)
KeywordsRNA BINDING PROTEIN/RNA / SmpB / tmRNA / SsrA RNA / 10Sa RNA / tRNA / trans-translation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


trans-translation / rRNA binding / cytoplasm
Similarity search - Function
Small Protein B; Chain: A; / Small protein B / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / SsrA-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsBessho, Y. / Shibata, R. / Sekine, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Authors: Bessho, Y. / Shibata, R. / Sekine, S. / Murayama, K. / Higashijima, K. / Hori-Takemoto, C. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJul 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SsrA-binding protein
C: SsrA-binding protein
E: SsrA-binding protein
G: SsrA-binding protein
B: tmRNA (63-MER)
D: tmRNA (63-MER)
F: tmRNA (63-MER)
H: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)137,8668
Polymers137,8668
Non-polymers00
Water0
1
A: SsrA-binding protein
B: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-6 kcal/mol
Surface area16330 Å2
MethodPISA
2
C: SsrA-binding protein
D: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-5 kcal/mol
Surface area16500 Å2
MethodPISA
3
E: SsrA-binding protein
F: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-6 kcal/mol
Surface area16800 Å2
MethodPISA
4
G: SsrA-binding protein
H: tmRNA (63-MER)


Theoretical massNumber of molelcules
Total (without water)34,4672
Polymers34,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-4 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.776, 67.957, 178.662
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
SsrA-binding protein


Mass: 14177.479 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RR57
#2: RNA chain
tmRNA (63-MER)


Mass: 20289.061 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Total 63nt of RNA was generated by binding T7 trascript (41nt) and chemically synthesized RNA (22nt).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2ammonium sulfate11
3ammonium sulfate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2004
RadiationMonochromator: double flat Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→48.76 Å / Num. obs: 40370 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.33 % / Rsym value: 0.075 / Net I/σ(I): 23.69
Reflection shellResolution: 3.01→3.11 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3977 / Rsym value: 0.366 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P6V, 1WJX

1p6v

1wjx


Resolution: 3.01→48.76 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS CRYSTAL HAS A PSEUDO-MEROHEDRAL PERFECT TWINNING. THE TWINNING OPERATER IS (H,K,L) -> (H,-K,-L). THE R-FACTOR IS 0.255 AND THE R-FREE IS 0.320 WHEN THIS TWINING OPERATOR IS USED WITH TWIN_LSQ TARGET.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 3034 7.4 %RANDOM
Rwork0.255 ---
obs-39488 96.7 %-
Displacement parametersBiso mean: 94.2 Å2
Refinement stepCycle: LAST / Resolution: 3.01→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 5292 0 0 9224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree: 0.375 / Rfactor Rwork: 0.361 / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.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