4IND | pdb_00004ind

The Triple Jelly Roll Fold and Turret Assembly in an Archaeal Virus

PDB DOI: https://doi.org/10.2210/pdb4IND/pdb

Classification: VIRAL PROTEIN
Organism(s): Sulfolobus turreted icosahedral virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-04 Released: 2013-01-23
Deposition Author(s): Eilers, B.J., Kraft, D., Burgess, M.C., Young, M.J., Lawrence, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Triple Jelly Roll Fold and Turret Assembly in an Archaeal Virus

Eilers, B.J., Kraft, D., Burgess, M.C., Young, M.J., Lawrence, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 856.53 kDa
Atom Count: 64,220
Modeled Residue Count: 7,540
Deposited Residue Count: 7,740
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C381 turret protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	387	Sulfolobus turreted icosahedral virus 1	Mutation(s): 0 Gene Names: C381
UniProt
Find proteins for Q6Q0L3 (Sulfolobus turreted icosahedral virus 1) Explore Q6Q0L3 Go to UniProtKB: Q6Q0L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6Q0L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2HP Query on 2HP Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth L] SDF format, chain DA [auth D] SDF format, chain DB [auth L] SDF format, chain FB [auth M] SDF format, chain NA [auth G] SDF format, chain SB [auth Q] SDF format, chain TB [auth Q] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain ZB [auth T] SDF format, chain ZA [auth K] SDF format, chain Z [auth B] SDF format, chain YB [auth S] SDF format, chain YA [auth K] SDF format, chain Y [auth B] SDF format, chain XB [auth S] SDF format, chain XA [auth J] SDF format, chain X [auth B] SDF format, chain WB [auth S] SDF format, chain WA [auth J] SDF format, chain W [auth A] SDF format, chain VB [auth R] SDF format, chain VA [auth I] SDF format, chain UB [auth R] SDF format, chain UA [auth I] SDF format, chain TA [auth I] SDF format, chain SA [auth I] SDF format, chain RB [auth Q] SDF format, chain RA [auth H] SDF format, chain QB [auth Q] SDF format, chain QA [auth H] SDF format, chain PB [auth P] SDF format, chain PA [auth H] SDF format, chain OB [auth P] SDF format, chain OA [auth G] SDF format, chain NB [auth P] SDF format, chain MB [auth O] SDF format, chain MA [auth G] SDF format, chain LB [auth O] SDF format, chain LA [auth F] SDF format, chain KB [auth O] SDF format, chain KA [auth F] SDF format, chain JB [auth N] SDF format, chain JA [auth F] SDF format, chain IB [auth N] SDF format, chain IA [auth E] SDF format, chain HB [auth N] SDF format, chain HA [auth E] SDF format, chain GB [auth M] SDF format, chain GA [auth E] SDF format, chain FA [auth D] SDF format, chain EB [auth M] SDF format, chain EA [auth D] SDF format, chain CB [auth L] SDF format, chain CA [auth C] SDF format, chain BC [auth T] SDF format, chain BA [auth C] SDF format, chain AC [auth T] SDF format, chain AA [auth B] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth L] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth L] MOL2 format, chain FB [auth M] MOL2 format, chain NA [auth G] MOL2 format, chain SB [auth Q] MOL2 format, chain TB [auth Q] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain ZB [auth T] MOL2 format, chain ZA [auth K] MOL2 format, chain Z [auth B] MOL2 format, chain YB [auth S] MOL2 format, chain YA [auth K] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth S] MOL2 format, chain XA [auth J] MOL2 format, chain X [auth B] MOL2 format, chain WB [auth S] MOL2 format, chain WA [auth J] MOL2 format, chain W [auth A] MOL2 format, chain VB [auth R] MOL2 format, chain VA [auth I] MOL2 format, chain UB [auth R] MOL2 format, chain UA [auth I] MOL2 format, chain TA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain RB [auth Q] MOL2 format, chain RA [auth H] MOL2 format, chain QB [auth Q] MOL2 format, chain QA [auth H] MOL2 format, chain PB [auth P] MOL2 format, chain PA [auth H] MOL2 format, chain OB [auth P] MOL2 format, chain OA [auth G] MOL2 format, chain NB [auth P] MOL2 format, chain MB [auth O] MOL2 format, chain MA [auth G] MOL2 format, chain LB [auth O] MOL2 format, chain LA [auth F] MOL2 format, chain KB [auth O] MOL2 format, chain KA [auth F] MOL2 format, chain JB [auth N] MOL2 format, chain JA [auth F] MOL2 format, chain IB [auth N] MOL2 format, chain IA [auth E] MOL2 format, chain HB [auth N] MOL2 format, chain HA [auth E] MOL2 format, chain GB [auth M] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth M] MOL2 format, chain EA [auth D] MOL2 format, chain CB [auth L] MOL2 format, chain CA [auth C] MOL2 format, chain BC [auth T] MOL2 format, chain BA [auth C] MOL2 format, chain AC [auth T] MOL2 format, chain AA [auth B] mmCIF format, chain AB [auth K] mmCIF format, chain BB [auth L] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth L] mmCIF format, chain FB [auth M] mmCIF format, chain NA [auth G] mmCIF format, chain SB [auth Q] mmCIF format, chain TB [auth Q] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain ZB [auth T] mmCIF format, chain ZA [auth K] mmCIF format, chain Z [auth B] mmCIF format, chain YB [auth S] mmCIF format, chain YA [auth K] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth S] mmCIF format, chain XA [auth J] mmCIF format, chain X [auth B] mmCIF format, chain WB [auth S] mmCIF format, chain WA [auth J] mmCIF format, chain W [auth A] mmCIF format, chain VB [auth R] mmCIF format, chain VA [auth I] mmCIF format, chain UB [auth R] mmCIF format, chain UA [auth I] mmCIF format, chain TA [auth I] mmCIF format, chain SA [auth I] mmCIF format, chain RB [auth Q] mmCIF format, chain RA [auth H] mmCIF format, chain QB [auth Q] mmCIF format, chain QA [auth H] mmCIF format, chain PB [auth P] mmCIF format, chain PA [auth H] mmCIF format, chain OB [auth P] mmCIF format, chain OA [auth G] mmCIF format, chain NB [auth P] mmCIF format, chain MB [auth O] mmCIF format, chain MA [auth G] mmCIF format, chain LB [auth O] mmCIF format, chain LA [auth F] mmCIF format, chain KB [auth O] mmCIF format, chain KA [auth F] mmCIF format, chain JB [auth N] mmCIF format, chain JA [auth F] mmCIF format, chain IB [auth N] mmCIF format, chain IA [auth E] mmCIF format, chain HB [auth N] mmCIF format, chain HA [auth E] mmCIF format, chain GB [auth M] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth M] mmCIF format, chain EA [auth D] mmCIF format, chain CB [auth L] mmCIF format, chain CA [auth C] mmCIF format, chain BC [auth T] mmCIF format, chain BA [auth C] mmCIF format, chain AC [auth T] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth K] AC [auth T] BA [auth C] BB [auth L] AA [auth B], AB [auth K], AC [auth T], BA [auth C], BB [auth L], BC [auth T], CA [auth C], CB [auth L], DA [auth D], DB [auth L], EA [auth D], EB [auth M], FA [auth D], FB [auth M], GA [auth E], GB [auth M], HA [auth E], HB [auth N], IA [auth E], IB [auth N], JA [auth F], JB [auth N], KA [auth F], KB [auth O], LA [auth F], LB [auth O], MA [auth G], MB [auth O], NA [auth G], NB [auth P], OA [auth G], OB [auth P], PA [auth H], PB [auth P], QA [auth H], QB [auth Q], RA [auth H], RB [auth Q], SA [auth I], SB [auth Q], TA [auth I], TB [auth Q], U [auth A], UA [auth I], UB [auth R], V [auth A], VA [auth I], VB [auth R], W [auth A], WA [auth J], WB [auth S], X [auth B], XA [auth J], XB [auth S], Y [auth B], YA [auth K], YB [auth S], Z [auth B], ZA [auth K], ZB [auth T]	DIHYDROGENPHOSPHATE ION H₂ O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth K] Focus chain AC [auth T] Focus chain BA [auth C] Focus chain BB [auth L] Focus chain BC [auth T] Focus chain CA [auth C] Focus chain CB [auth L] Focus chain DA [auth D] Focus chain DB [auth L] Focus chain EA [auth D] Focus chain EB [auth M] Focus chain FA [auth D] Focus chain FB [auth M] Focus chain GA [auth E] Focus chain GB [auth M] Focus chain HA [auth E] Focus chain HB [auth N] Focus chain IA [auth E] Focus chain IB [auth N] Focus chain JA [auth F] Focus chain JB [auth N] Focus chain KA [auth F] Focus chain KB [auth O] Focus chain LA [auth F] Focus chain LB [auth O] Focus chain MA [auth G] Focus chain MB [auth O] Focus chain NA [auth G] Focus chain NB [auth P] Focus chain OA [auth G] Focus chain OB [auth P] Focus chain PA [auth H] Focus chain PB [auth P] Focus chain QA [auth H] Focus chain QB [auth Q] Focus chain RA [auth H] Focus chain RB [auth Q] Focus chain SA [auth I] Focus chain SB [auth Q] Focus chain TA [auth I] Focus chain TB [auth Q] Focus chain U [auth A] Focus chain UA [auth I] Focus chain UB [auth R] Focus chain V [auth A] Focus chain VA [auth I] Focus chain VB [auth R] Focus chain W [auth A] Focus chain WA [auth J] Focus chain WB [auth S] Focus chain X [auth B] Focus chain XA [auth J] Focus chain XB [auth S] Focus chain Y [auth B] Focus chain YA [auth K] Focus chain YB [auth S] Focus chain Z [auth B] Focus chain ZA [auth K] Focus chain ZB [auth T] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth K] Focus chain AC [auth T] Focus chain BA [auth C] Focus chain BB [auth L] Focus chain BC [auth T] Focus chain CA [auth C] Focus chain CB [auth L] Focus chain DA [auth D] Focus chain DB [auth L] Focus chain EA [auth D] Focus chain EB [auth M] Focus chain FA [auth D] Focus chain FB [auth M] Focus chain GA [auth E] Focus chain GB [auth M] Focus chain HA [auth E] Focus chain HB [auth N] Focus chain IA [auth E] Focus chain IB [auth N] Focus chain JA [auth F] Focus chain JB [auth N] Focus chain KA [auth F] Focus chain KB [auth O] Focus chain LA [auth F] Focus chain LB [auth O] Focus chain MA [auth G] Focus chain MB [auth O] Focus chain NA [auth G] Focus chain NB [auth P] Focus chain OA [auth G] Focus chain OB [auth P] Focus chain PA [auth H] Focus chain PB [auth P] Focus chain QA [auth H] Focus chain QB [auth Q] Focus chain RA [auth H] Focus chain RB [auth Q] Focus chain SA [auth I] Focus chain SB [auth Q] Focus chain TA [auth I] Focus chain TB [auth Q] Focus chain U [auth A] Focus chain UA [auth I] Focus chain UB [auth R] Focus chain V [auth A] Focus chain VA [auth I] Focus chain VB [auth R] Focus chain W [auth A] Focus chain WA [auth J] Focus chain WB [auth S] Focus chain X [auth B] Focus chain XA [auth J] Focus chain XB [auth S] Focus chain Y [auth B] Focus chain YA [auth K] Focus chain YB [auth S] Focus chain Z [auth B] Focus chain ZA [auth K] Focus chain ZB [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.188 (Depositor), 0.189 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.774	α = 81.84
b = 166.999	β = 82.17
c = 186.975	γ = 81.44

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-23
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description