[English] 日本語
Yorodumi
- PDB-2nsa: Structures of and interactions between domains of trigger factor ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nsa
TitleStructures of and interactions between domains of trigger factor from Themotoga maritim
ComponentsTrigger factor
KeywordsCHAPERONE
Function / homology
Function and homology information


'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / cell cycle ...'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / cell cycle / cell division / DNA binding / cytoplasm
Similarity search - Function
Trigger factor, domain 2 / Trigger factor, C-terminal domain / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / 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 / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS, native anomalous / SIRAS / Resolution: 1.7 Å
AuthorsMartinez-Hackert, E. / Hendrickson, W.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of and interactions between domains of trigger factor from Thermotoga maritima.
Authors: Martinez-Hackert, E. / Hendrickson, W.A.
History
DepositionNov 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Trigger factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7404
Polymers20,4521
Non-polymers2883
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Trigger factor
hetero molecules

A: Trigger factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4808
Polymers40,9042
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3720 Å2
ΔGint-101 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.840, 74.210, 90.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Trigger factor / TF


Mass: 20451.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tig / Plasmid: pet24d / Production host: Escherichia coli (E. coli) / Strain (production host): RIL codon-plus / References: UniProt: Q9WZF8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 1.35M ammonium sulfate 0.05M TrisCl, pH 7.4, VAPOR DIFFUSION, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21101
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONNSLS X4A10.979
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDFeb 19, 2002monochromator
RIGAKU RAXIS IV2IMAGE PLATEFeb 26, 2002mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromator with a sagittally focused second crystal.SINGLE WAVELENGTHMx-ray1
2Lab designed mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.54181
Reflection

D res low: 20 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)% possible obs
1201700.0431.991.799.7
2.8266360.031.2522.489.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.662099.310.0391.817
2.93.6610010.0431.844
2.542.999.610.0462.09
2.312.5499.710.052.198
2.142.3199.810.0552.253
2.022.1499.910.0612.156
1.912.0299.810.0752.04
1.831.9199.910.0951.962
1.761.8399.610.1211.921
1.71.7699.810.1571.874
4.972083.820.0251.317
3.954.9789.320.0251.241
3.463.959120.0281.309
3.143.469320.0311.162
2.923.1492.120.0371.264
2.752.9293.220.0421.146
2.612.7592.720.0481.289
2.52.6193.220.0521.291
2.42.581.720.0541.245
ReflectionResolution: 1.7→20 Å / Num. all: 20204 / Num. obs: 20170 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.157 / % possible all: 99.8

-
Phasing

PhasingMethod: SIRAS
Phasing setD res high: 1.7 Å / D res low: 19.6 Å
Phasing dmFOM : 0.52 / FOM acentric: 0.51 / FOM centric: 0.56 / Reflection: 19614 / Reflection acentric: 17762 / Reflection centric: 1852
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.9-19.6070.940.940.89917694223
3-4.90.930.930.8827302343387
2.4-30.80.810.6933593017342
2.1-2.40.60.610.533683089279
1.8-2.10.290.30.2657775366411
1.7-1.80.110.110.0934633253210
Phasing MIR derResolution: 1.7→19.6 Å
Phasing MIR der site

Der-ID: 1

IDBiso (Å)Cartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolOccupancy
146.112.5089.05417.496SE0.5
232.410.70712.36515.244SE0.28
317.142.16229.139.178I0.19
41636.2335.7487.139I0.15
530.148.67411.31817.072I0.15

-
Processing

Software
NameVersionClassificationNB
SOLVEphasing
RESOLVE2.08phasing
CNSrefinement
PDB_EXTRACT1.401data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS, native anomalous / Resolution: 1.7→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1003 5 %random
Rwork0.227 ---
all-20170 --
obs-19614 97.1 %-
Displacement parametersBiso mean: 59.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.987 Å20 Å20 Å2
2--0.272 Å20 Å2
3---0.715 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 15 208 1629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004201
X-RAY DIFFRACTIONc_angle_deg0.88944

+
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://pdbjlvh1.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