[English] 日本語
Yorodumi
- PDB-1oms: Structure determination by MAD: E.coli Trigger Factor binding at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oms
TitleStructure determination by MAD: E.coli Trigger Factor binding at the ribosomal exit tunnel.
ComponentsTrigger Factor
KeywordsISOMERASE / alpha-beta structure
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat / cell cycle / cell division / membrane / identical protein binding / cytosol
Similarity search - Function
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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. ...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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SULFUR DIOXIDE / Trigger factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKristensen, O. / Gajhede, M.
Citation
Journal: Structure / Year: 2003
Title: Chaperone binding at the ribosomal exit tunnel.
Authors: Kristensen, O. / Gajhede, M.
#1: Journal: Nature / Year: 2002
Title: L23 protein functions as a chaperone docking site on the ribosome.
Authors: Kramer, G. / Rauch, T. / Rist, W. / Vorderwulbecke, S. / Patzelt, H. / Schulze-Specking, A. / Ban, N. / Deuerling, E. / Bukau, B.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Localization of the Trigger Factor Binding Site on the Ribosomal 50S Subunit.
Authors: Blaha, G. / Wilson, D.N. / Stoller, G. / Fischer, G. / Willumeit, R. / Nierhaus, K.H.
#3: Journal: J.Mol.Biol. / Year: 2003
Title: Interaction of trigger factor with the ribosome.
Authors: Maier, R. / Eckert, B. / Scholz, C. / Lilie, H. / Schmid, F.X.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trigger Factor
B: Trigger Factor
C: Trigger Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,89123
Polymers40,5153
Non-polymers2,37620
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-153 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.644, 71.644, 375.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-601-

SO2

21B-601-

SO2

31B-622-

HOH

41B-639-

HOH

51C-543-

HOH

61C-594-

HOH

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Trigger Factor


Mass: 13504.907 Da / Num. of mol.: 3 / Fragment: Ribosome binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tig / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A850, peptidylprolyl isomerase

-
Non-polymers , 5 types, 234 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-SO2 / SULFUR DIOXIDE / Sulfur dioxide


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.16 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 2000 MME, PEG 400, ammonium sulfate, sodium acetate, tris, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mg/mlprotein1drop
230 %PEG2000 MME1reservoir
385 mMsodium acetate1reservoir
4100 mMTris-base1reservoir
515 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9797, 0.9404
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2002
RadiationMonochromator: sagittal-focusing double crystal monochromator in combination with a vertical focusing mirror.
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.94041
ReflectionResolution: 2.3→30 Å / Num. obs: 17023 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 33.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2432 / Rsym value: 0.33 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 31810 / Redundancy: 4.2 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.33

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5499572.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement was based on the "mlhl" target function. Experimental phases and strong NCS restraints were used throughout. Used all data in the ultimate brief refinement cycle against a ...Details: Refinement was based on the "mlhl" target function. Experimental phases and strong NCS restraints were used throughout. Used all data in the ultimate brief refinement cycle against a standard crystallographic target: R-factor(all).
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2044 6.4 %SHELLS
Rwork0.208 ---
obs0.208 31810 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9718 Å2 / ksol: 0.353647 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å23.96 Å20 Å2
2--4.66 Å20 Å2
3----9.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 139 214 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 305 5.7 %
Rwork0.245 5011 -
obs-5011 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SO2.PARAMSO2.TOP
X-RAY DIFFRACTION5PG4.PARAMPG4.TOP
X-RAY DIFFRACTION6GOL.PARAMGOL.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

+
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