[English] 日本語
Yorodumi
- PDB-2f5g: Crystal structure of IS200 transposase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f5g
TitleCrystal structure of IS200 transposase
ComponentsTransposase, putative
KeywordsGENE REGULATION / Dimer / Stem-loop binding
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding
Similarity search - Function
Transposase IS200 like / Transposase IS200-like / Transposase IS200-like / Transposase IS200-like superfamily / Transposase IS200 like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transposase, putative
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsLee, H.H. / Yoon, J.Y. / Kim, H.S. / Kang, J.Y. / Kim, K.H. / Kim, D.J. / Suh, S.W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of a Metal Ion-bound IS200 Transposase
Authors: Lee, H.H. / Yoon, J.Y. / Kim, H.S. / Kang, J.Y. / Kim, K.H. / Kim, D.J. / Ha, J.Y. / Mikami, B. / Yoon, H.J. / Suh, S.W.
History
DepositionNov 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transposase, putative
B: Transposase, putative


Theoretical massNumber of molelcules
Total (without water)31,4362
Polymers31,4362
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-25 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.543, 68.149, 65.490
Angle α, β, γ (deg.)90.00, 129.24, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Transposase, putative / / IS200 transposase


Mass: 15718.204 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q97Y68
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 297 K / Method: evaporation / pH: 7.5
Details: 1.4M tri-sodium citrate, 100mM sodium HEPES (pH 7.5), EVAPORATION, temperature 297K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL38B110.8
SYNCHROTRONPAL/PLS 4A20.97960, 0.97972, 0.97192
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJul 15, 2005mirrors
ADSC QUANTUM 2102CCDApr 6, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
20.97961
30.979721
40.971921
ReflectionResolution: 1.7→30 Å / Num. obs: 34831 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 95.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→26.55 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 543905.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3457 10.1 %RANDOM
Rwork0.213 ---
obs0.213 34208 97.5 %-
all-34831 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2116 Å2 / ksol: 0.382152 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.5 Å20 Å22.04 Å2
2---3.15 Å20 Å2
3----2.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 0 308 2470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 565 10.2 %
Rwork0.238 4980 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.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