Mass: 16135.430 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 185-328 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PEG041 / Production host: Escherichia coli (E. coli) / References: UniProt: P77173
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
2
3D 13C-separated NOESY
1
2
3
3D 15N-separated NOESY
1
3
3
HNHA
1
4
3
2D 15N HSQC
NMR details
Text: The structure was determined using triple-resonance NMR spectroscopy. refinement program: x-plor V3.840, authors: brunger
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM ZipA U-15N,13C; 50mM phosphate buffer; 2 mM NaN3; 50 mM KCl; 90% H2O, 10% D2O; pH 5.5
90% H2O/10% D2O
2
1 mM ZipA U-15N,13C; 50mM phosphate buffer; 2 mM NaN3; 50 mM KCl; 100% D2O; pH 5.5
100% D2O
3
1 mM ZipA U-15N; 50mM phosphate buffer; 2 mM NaN3; 50 mM KCl; 90% H2O, 10% D2O; pH 5.5
90% H2O/10% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
50mMKCl
5.5
ambient
298K
2
50mMKCl
5.5
ambient
298K
3
50mMKCl
5.5
ambient
298K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
NMR spectrometer
Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz
-
Processing
NMR software
Name
Version
Developer
Classification
X-PLOR
V3.840
Brunger
structuresolution
NMRPipe
1.7
Delaglio
processing
PIPP
4.2.8
Garrett
dataanalysis
XwinNMR
2
Bruker
collection
X-PLOR
V3.840
Brunger
refinement
Refinement
Method: distance geometry simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 2758 restraints, 2038 are NOE-derived distance constraints, 377 dihedral angle restraints, 84 distance restraints from hydrogen bonds, 113 3JNHa ...Details: The structures are based on a total of 2758 restraints, 2038 are NOE-derived distance constraints, 377 dihedral angle restraints, 84 distance restraints from hydrogen bonds, 113 3JNHa coupling restraints, 230 secondary Ca/Cb chemical shift restraints, and a conformational database. The coordinates in this entry corrospond to the refined minimized average structure determined from an ensemble of 30 structures
NMR representative
Selection criteria: nmr, minimized average structure
NMR ensemble
Conformers submitted total number: 1
+
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