- PDB-1ehx: NMR SOLUTION STRUCTURE OF THE LAST UNKNOWN MODULE OF THE CELLULOS... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1ehx
Title
NMR SOLUTION STRUCTURE OF THE LAST UNKNOWN MODULE OF THE CELLULOSOMAL SCAFFOLDIN PROTEIN CIPC OF CLOSTRIDUM CELLULOLYTICUM
Components
SCAFFOLDIN PROTEIN
Keywords
UNKNOWN FUNCTION / beta-beta-barrels / 3.10 helix
Function / homology
Function and homology information
hydrolase activity, acting on glycosyl bonds / cellulose binding / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function
back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Representative
-
Components
#1: Protein
SCAFFOLDINPROTEIN / CIPC
Mass: 10042.232 Da / Num. of mol.: 1 / Fragment: UNKNOW DOMAIN / Source method: isolated from a natural source / Details: HOMOLOGOUS MODULE WITH UNKNOW FUNCTION X2 / Source: (natural) Clostridium cellulolyticum (bacteria) / References: UniProt: Q45996
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
1
3D 15N-separated NOESY
1
3
1
DQF-COSY
1
4
1
2D 15N HSQC
1
5
1
2D 15N HSQCNOESY
1
6
1
2D 15N HSQCTOCSY
-
Sample preparation
Details
Contents: 25 mM X2 uniform labelling 15N; 20 mM acetate buffer Na; 90% H2O, 10% D2O
Sample conditions
pH: 5.0 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
NMR spectrometer
Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz
-
Processing
NMR software
Name
Version
Classification
XwinNMR
2.1
processing
XEASY
1.2
dataanalysis
DIANA
2.8
structuresolution
CNS
1
refinement
Refinement
Method: distance geometry, simulated annealing, torsion angle dynamics Software ordinal: 1 Details: the structures are based on a total of 1828 restraints, 1647 are NOE-derived distance constraints, 66 dihedral angle restraints, 105 distance restraints from hydrogen bonds
NMR ensemble
Conformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20
+
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