[English] 日本語
Yorodumi
- PDB-6sy0: Structure of the Plasmodium falciparum SIP2 DNA-binding AP2 tande... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sy0
TitleStructure of the Plasmodium falciparum SIP2 DNA-binding AP2 tandem repeat in complex with two SPE2 half-sites
Components
  • DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
  • Transcription factor with AP2 domain(S)
KeywordsDNA BINDING PROTEIN / Plasmodium falciparum malaria Subtelomeric repeat var genes
Function / homologytelomeric DNA binding / nuclear periphery / DNA / DNA (> 10) / AP2 domain transcription factor
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.102 Å
AuthorsReiter, D. / Kantsadi, A. / Vakonakis, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Structural and functional analysis of the Plasmodium falciparum SIP2 DNA binding domain
Authors: Niederwieser, I. / Reiter, D. / Kantsadi, A. / Voss, T. / Vakonakis, I.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription factor with AP2 domain(S)
B: Transcription factor with AP2 domain(S)
C: Transcription factor with AP2 domain(S)
E: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
F: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
K: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
L: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)82,9609
Polymers82,9609
Non-polymers00
Water00
1
B: Transcription factor with AP2 domain(S)
E: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,6533
Polymers27,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcription factor with AP2 domain(S)
F: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
G: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,6533
Polymers27,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-21 kcal/mol
Surface area14350 Å2
MethodPISA
3
C: Transcription factor with AP2 domain(S)
K: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')
L: DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,6533
Polymers27,6533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-14 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.350, 43.720, 153.710
Angle α, β, γ (deg.)90.00, 92.17, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein Transcription factor with AP2 domain(S)


Mass: 16618.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0604100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6KSN9
#2: DNA chain
DNA (5'-D(*GP*GP*TP*GP*CP*AP*CP*CP*TP*AP*GP*GP*TP*GP*CP*AP*CP*C)-3')


Mass: 5517.566 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote)
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.16 M calcium acetate 100 mM cacodylic acid 6.5% w/v PEG 8000 20% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 3.1→153.6 Å / Num. obs: 19852 / % possible obs: 97 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Net I/σ(I): 15.24
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8 % / Rmerge(I) obs: 1.088 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 1912 / CC1/2: 0.927 / Rrim(I) all: 1.164 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.102→43.931 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3184 963 5 %0
Rwork0.2736 ---
obs0.2758 18302 96.72 %-
Refinement stepCycle: LAST / Resolution: 3.102→43.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 2196 0 0 5331

+
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