4XR1 | Genus

Total Genus 88

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	88
sequence length	307
structure length	307
Chain Sequence	RYDLVDRLNTTFRQMEQELAIFAAHLEQHKLLVARVFSLPEVKKEDEHNPLNRIEVKQHLGNDAQSLALRHFRHLFIQQQSENRSSKAAVRLPGVLCYQVDNLSQAALVSHIQHINKLKTTFEHIVTVESELPTAARFEWVHRHLPGLITLNAYRTLTVLHDPATLRFGWANKHIIKNLHRDEVLAQLEKSLKSPRSVAPWTREEWQRKLEREYQDIAALPQNAKLKIKRPVKVQPIARVWYKGDQKQVQHACPTPLIALINRDNGAGVPDVGELLNYDADNVQHRYKPQAQPLRLIIPRLHLYVAD

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__4137337865629873__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__4137337865629873__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4xr1/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__4137337865629873__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"4137337865629873","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4xr1/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__4137337865629873__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d14b76f61a12ee25ec51791/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d14b76f61a12ee25ec51791/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d14b76f61a12ee25ec51791/pdb.gz)

loadScript /static/js/j2s/core/corezip.z.js

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5d14b76f61a12ee25ec51791/pdb.gz): 292 ms

reading 307 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

307 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 25 ms

Adding embedded #jmolscript: select ({0:306});backbone only;select *;

platformSpeed = 8

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

loadScript /static/js/j2s/core/corescriptcmd.z.js

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

loadScript /static/js/j2s/J/g3d/HermiteRenderer.js

loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Replication/dna
source organism	Escherichia coli (strain k12)
publication title	Replisome speed determines the efficiency of the Tus-Ter replication termination barrier. pubmed doi rcsb
molecule keywords	DNA replication terminus site-binding protein
total genus	88
structure length	307
sequence length	307
ec nomenclature
pdb deposition date	2015-01-20

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF05472	Ter	DNA replication terminus site-binding protein (Ter protein)

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
3.30.54.10	Alpha Beta	2-Layer Sandwich	Replication Terminator Protein; Chain A, domain 2	Replication Terminator Protein; Chain A, domain 2	4xr1A02
3.50.14.10	Alpha Beta	3-Layer(bba) Sandwich	Replication Terminator Protein (Tus); Chain A, domain 1	Replication terminator Tus, domain 1 superfamily/Replication terminator Tus	4xr1A01

4XR1A 4XR3A 1ECRA 4XR2A 2I05A 2EWJA 4XR0A 2I06A
chains in the Genus database with same CATH superfamily

2ZZFA 1TKYA 3WQZA 3RFNA 2I05A 1V4PA 1WNUA 1V7OA 2ZZGA 4XR3A 4XR1A 2ZTGA 3RHUA 4XR0A 2EWJA 1TKEA 1QF6A 4XR2A 1TKGA 2I06A 1TJEA 1WXOA 1ECRA 2ZZEA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4XR1 A;  4XR3 A;  1ECR A;  4XR2 A;  2I05 A;  2EWJ A;  4XR0 A;  2I06 A; 
#chains in the Genus database with same CATH topology
 2ZZF A;  1TKY A;  3WQZ A;  3RFN A;  2I05 A;  1V4P A;  1WNU A;  1V7O A;  2ZZG A;  4XR3 A;  4XR1 A;  2ZTG A;  3RHU A;  4XR0 A;  2EWJ A;  1TKE A;  1QF6 A;  4XR2 A;  1TKG A;  2I06 A;  1TJE A;  1WXO A;  1ECR A;  2ZZE A; 
#chains in the Genus database with same CATH homology
 2ZZF A;  1TKY A;  3WQZ A;  3RFN A;  2I05 A;  1V4P A;  1WNU A;  1V7O A;  2ZZG A;  4XR3 A;  4XR1 A;  2ZTG A;  3RHU A;  4XR0 A;  2EWJ A;  1TKE A;  1QF6 A;  4XR2 A;  1TKG A;  2I06 A;  1TJE A;  1WXO A;  1ECR A;  2ZZE A;

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

4XR1A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations