[English] 日本語
Yorodumi
- PDB-1t11: Trigger Factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t11
TitleTrigger Factor
ComponentsTrigger factor
KeywordsCHAPERONE / helix-turn-helix / four-helix-bundle / PPIase
Function / homology
Function and homology information


'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein folding / protein transport / cell cycle ...'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein folding / protein transport / cell cycle / cell division / cytoplasm
Similarity search - Function
Trigger factor, domain 2 / Trigger factor, C-terminal domain / Trigger factor ribosome-binding domain / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily ...Trigger factor, domain 2 / Trigger factor, C-terminal domain / Trigger factor ribosome-binding domain / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLudlam, A.V. / Moore, B.A. / Xu, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The crystal structure of ribosomal chaperone trigger factor from Vibrio cholerae.
Authors: Ludlam, A.V. / Moore, B.A. / Xu, Z.
History
DepositionApr 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trigger factor
B: Trigger factor


Theoretical massNumber of molelcules
Total (without water)86,9612
Polymers86,9612
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-22 kcal/mol
Surface area38910 Å2
MethodPISA
2
A: Trigger factor
B: Trigger factor

A: Trigger factor
B: Trigger factor


Theoretical massNumber of molelcules
Total (without water)173,9224
Polymers173,9224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_645-x+1,-y-1,z1
Buried area11480 Å2
ΔGint-76 kcal/mol
Surface area73690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.860, 189.860, 62.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsThe biological assembly is a dimer as represented in the asymmetric unit

-
Components

#1: Protein Trigger factor / TF


Mass: 43480.574 Da / Num. of mol.: 2 / Fragment: TF truncation (residues 1-389)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: TIG, VC1923 / Plasmid: pSJ4 (modified pET21a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQS5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.26862Structure factor file contains Friedel's pairs
2Structure factor file contains Friedel's pairs
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop8.5ammonium sulfate, tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop9.5malonate, glycine, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B10.9498
SYNCHROTRONAPS 5ID-B20.9796, 0.9797, 1.0034
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJul 19, 2003
MARRESEARCH2CCDJul 19, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1APS mirrorsSINGLE WAVELENGTHMx-ray1
2APS mirrorsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.94981
20.97961
30.97971
41.00341
ReflectionResolution: 2.5→44.75 Å / Num. obs: 78740 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 35.8 Å2 / Rsym value: 0.052 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.16 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3512 / Rsym value: 0.364 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
d*TREKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: Malonate crystal form solved with MAD (unpublished). Incomplete model from malonate form used for molecular replacement of ammonium sulfate data.

Resolution: 2.5→44.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 195581.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel's pairs were used
RfactorNum. reflection% reflectionSelection details
Rfree0.29 6760 9.7 %RANDOM
Rwork0.239 ---
all-69335 --
obs-69335 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8252 Å2 / ksol: 0.337212 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.18 Å20 Å20 Å2
2--4.18 Å20 Å2
3----8.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 0 108 5898
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 952 9.2 %
Rwork0.367 9397 -
obs-9397 83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

+
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