Mass: 8486.523 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding domain residues 62-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PITX3, PTX3 / Production host: Escherichia coli (E. coli) / References: UniProt: O75364, UniProt: Q99697*PLUS
#2: DNA chain
DNA (5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3')
Mass: 3887.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain
DNA (5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3')
Mass: 4056.646 Da / Num. of mol.: 1 / Source method: obtained synthetically
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
2
2D 1H-15N HSQC
1
2
2
3D 1H-15N NOESY
1
3
1
2D 1H-13C HSQC aliphatic
1
4
1
2D 1H-13C HSQC aromatic
1
5
1
3DCBCA(CO)NH
1
6
1
3DC(CO)NH
1
7
1
3D HNCO
1
8
1
3D HNCA
1
9
1
3D HN(CA)CB
1
10
1
3DH(CCO)NH
1
11
1
3D (H)CCH-TOCSY
1
12
1
3D 1H-13C NOESY aliphatic
1
13
1
3D 1H-13C NOESY aromatic
1
14
1
3DHBHA(CO)NH
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM [U-99% 13C; U-99% 15N] pitx2 homeodomain, 1 mM DNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3'), 1 mM DNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3'), 90% H2O/10% D2O
90% H2O/10% D2O
2
1 mM [U-99% 15N] pitx2 homeodomain, 1 mM DNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3'), 1 mM DNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3'), 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1mM
pitx2 homeodomain-1
[U-99% 13C; U-99% 15N]
1
1mM
DNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3')-2
1
1mM
DNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3')-3
1
1mM
pitx2 homeodomain-4
[U-99% 15N]
2
1mM
DNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3')-5
2
1mM
DNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3')-6
2
Sample conditions
pH: 7 / Pressure: ambient / Temperature: 295 K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
800
1
Varian INOVA
Varian
INOVA
600
2
Varian INOVA
Varian
INOVA
500
3
-
Processing
NMR software
Name
Developer
Classification
CYANA
Guntert, MumenthalerandWuthrich
structuresolution
Amber
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, andKollm
refinement
Refinement
Method: molecular dynamics / Software ordinal: 1
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 30 / Conformers submitted total number: 17
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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