BMRB Entry 17897

Name: NOE-based 3D structure of the monomeric partially-folded intermediate of CylR2 at 259K (-14 Celsius degrees)
Published: 2013-02-15

Click here to enlarge.

PDB ID: 2lyr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17897
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title: NOE-based 3D structure of the monomeric partially-folded intermediate of CylR2 at 259K (-14 Celsius degrees) PubMed: 23396077

Deposition date: 2011-08-29 Original release date: 2013-02-15

Authors: Jaremko, Mariusz; Jaremko, Lukasz; Kim, Hai-Young; Cho, Min-Kyu; Schwieters, Charles; Giller, Karin; Becker, Stefan; Zweckstetter, Markus

Citation: Jaremko, Mariusz; Jaremko, Lukasz; Kim, Hai-Young; Cho, Min-Kyu; Schwieters, Charles; Giller, Karin; Becker, Stefan; Zweckstetter, Markus. "Cold denaturation of a protein dimer monitored at atomic resolution." Nat. Chem. Biol. 9, 264-270 (2013).

Assembly members:
CylR2, polymer, 66 residues, 7725.070 Da.

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
CylR2: MIINNLKLIREKKKISQSEL AALLEVSRQTINGIEKNKYN PSLQLALKIAYYLNTPLEDI FQWQPE

Study: Cold denaturation of the CylR2 homodimer monitored at atomic resolution.

25 °C	-3 °C	-7 °C Dimer	-7 °C Monomer	-11 °C	-14 °C	-16 °C
17892	17893	17894	17895	17896	17897	17898
2lyj	2lyk	2lyl	2lyp	2lyq	2lyr	2lys

call loadScript special\jsmol\core\package.js

call loadScript special\jsmol\core\core.z.js -- required by ClazzNode

Jmol JavaScript applet jmolApplet0_object__806155015379193__ initializing

getValue debug = null

getValue logLevel = null

AppletRegistry.checkIn(jmolApplet0_object__806155015379193__)

viewerOptions:

{ "name":"jmolApplet0_object","applet":true,"documentBase":"http://bmrb.protein.osaka-u.ac.jp/data_library/summary/index.php?bmrbId=17897","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0_object__806155015379193__","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol.MyStatusListener object]","codeBase":"http://bmrb.protein.osaka-u.ac.jp/data_library/summary/special/jsmol/j2s/","syncId":"806155015379193","bgcolor":"white" }

Jmol Version: 13.1.14_dev24 $Date: 2013/04/12 03:24:02 $

java.vendor: j2s

java.version: 0.0

os.name: j2s

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0_object (signed)

starting HoverWatcher_1

getValue emulate = null

defaults = "Jmol"

getValue boxbgcolor = null

getValue bgcolor = white

backgroundColor = "white"

getValue ANIMFRAMECallback = null

getValue APPLETREADYCallback = Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

getValue ATOMMOVEDCallback = null

getValue CLICKCallback = null

getValue ECHOCallback = null

getValue ERRORCallback = null

getValue EVALCallback = null

getValue HOVERCallback = null

getValue LOADSTRUCTCallback = null

getValue MEASURECallback = null

getValue MESSAGECallback = null

getValue MINIMIZATIONCallback = null

getValue PICKCallback = null

getValue RESIZECallback = null

getValue SCRIPTCallback = null

getValue SYNCCallback = null

getValue doTranslate = null

language=en_US

getValue popupMenu = null

getValue script = null

Jmol applet jmolApplet0_object__806155015379193__ ready

call loadScript special\jsmol\core\corescript.z.js

starting QueueThread0_2

script 1 started

call loadScript special\jsmol\core\corestate.z.js

FileManager.getAtomSetCollectionFromFile(special/get_rep_pdb.php?pdb=2lyj)

starting HoverWatcher_3

FileManager opening http://bmrb.protein.osaka-u.ac.jp/data_library/summary/special/get_rep_pdb.php?pdb=2lyj

Time for openFile(special/get_rep_pdb.php?pdb=2lyj): 1257 ms

File Error:unrecognized file format for file http://bmrb.protein.osaka-u.ac.jp/data_library/summary/special/get_rep_pdb.php?pdb=2lyj

Could not find PDB file for that entry.

starting HoverWatcher_4

script ERROR: unrecognized file format for file http://bmrb.protein.osaka-u.ac.jp/data_library/summary/special/get_rep_pdb.php?pdb=2lyj

Could not find PDB file for that entry.

----

load >> "special/get_rep_pdb.php?pdb=2lyj" <<

Script completed

Jmol script terminated

25°C -16°C

Adapted by permission from Macmillan Publishers Ltd: Nature Chemical Biology, copyright 2013

Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).
UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.
JSmol: an open-source HTML5 viewer for chemical structures in 3D.

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	168
15N chemical shifts	67
1H chemical shifts	381

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

BMRB	17892 17893 17894 17895 17896 17898
PDB	1UTX 2GZU 2LYJ 2LYK 2LYL 2LYP 2LYQ 2LYR 2LYS 2XI8 2XIU 2XJ3
GB	AAL59476 AAL60140 AAM75247 AAO80372 AIL03173
REF	NP_814301 WP_002358483 WP_002370931 WP_010773902 WP_048951311

Biological Magnetic Resonance Data Bank

BMRB Entry 17897

Title: NOE-based 3D structure of the monomeric partially-folded intermediate of CylR2 at 259K (-14 Celsius degrees) PubMed: 23396077

Study: Cold denaturation of the CylR2 homodimer monitored at atomic resolution.

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links: