3ZTE | pdb_00003zte

Crystal Structure of the TRP RNA-Binding Attenuation Protein (TRAP) from Bacillus Licheniformis.

PDB DOI: https://doi.org/10.2210/pdb3ZTE/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Bacillus licheniformis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-07 Released: 2011-10-12
Deposition Author(s): Shevtsov, M.B., Chen, Y., Gollnick, P., Antson, A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.346 (Depositor), 0.341 (DCC)
R-Value Work:
0.281 (Depositor), 0.276 (DCC)
R-Value Observed:
0.284 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Trp RNA-Binding Attenuation Protein (Trap) from Bacillus Licheniformis.

Shevtsov, M.B., Chen, Y., Gollnick, P., Antson, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 195.45 kDa
Atom Count: 12,416
Modeled Residue Count: 1,522
Deposited Residue Count: 1,716
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)	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, U, V	78	Bacillus licheniformis	Mutation(s): 0
UniProt
Find proteins for A5A665 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore A5A665 Go to UniProtKB: A5A665
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5A665
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRP Query on TRP Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth C] SDF format, chain X [auth B] SDF format, chain W [auth A] SDF format, chain RA [auth V] SDF format, chain QA [auth U] SDF format, chain PA [auth T] SDF format, chain OA [auth S] SDF format, chain NA [auth R] SDF format, chain MA [auth Q] SDF format, chain LA [auth P] SDF format, chain KA [auth O] SDF format, chain JA [auth N] SDF format, chain IA [auth M] SDF format, chain HA [auth L] SDF format, chain GA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth I] SDF format, chain DA [auth H] SDF format, chain CA [auth G] SDF format, chain BA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth B] MOL2 format, chain W [auth A] MOL2 format, chain RA [auth V] MOL2 format, chain QA [auth U] MOL2 format, chain PA [auth T] MOL2 format, chain OA [auth S] MOL2 format, chain NA [auth R] MOL2 format, chain MA [auth Q] MOL2 format, chain LA [auth P] MOL2 format, chain KA [auth O] MOL2 format, chain JA [auth N] MOL2 format, chain IA [auth M] MOL2 format, chain HA [auth L] MOL2 format, chain GA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth B] mmCIF format, chain W [auth A] mmCIF format, chain RA [auth V] mmCIF format, chain QA [auth U] mmCIF format, chain PA [auth T] mmCIF format, chain OA [auth S] mmCIF format, chain NA [auth R] mmCIF format, chain MA [auth Q] mmCIF format, chain LA [auth P] mmCIF format, chain KA [auth O] mmCIF format, chain JA [auth N] mmCIF format, chain IA [auth M] mmCIF format, chain HA [auth L] mmCIF format, chain GA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth F] CA [auth G] DA [auth H] EA [auth I] AA [auth E], BA [auth F], CA [auth G], DA [auth H], EA [auth I], FA [auth J], GA [auth K], HA [auth L], IA [auth M], JA [auth N], KA [auth O], LA [auth P], MA [auth Q], NA [auth R], OA [auth S], PA [auth T], QA [auth U], RA [auth V], W [auth A], X [auth B], Y [auth C], Z [auth D]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain JA [auth N] Focus chain KA [auth O] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain NA [auth R] Focus chain OA [auth S] Focus chain PA [auth T] Focus chain QA [auth U] Focus chain RA [auth V] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain GA [auth K] Focus chain HA [auth L] Focus chain IA [auth M] Focus chain JA [auth N] Focus chain KA [auth O] Focus chain LA [auth P] Focus chain MA [auth Q] Focus chain NA [auth R] Focus chain OA [auth S] Focus chain PA [auth T] Focus chain QA [auth U] Focus chain RA [auth V] Focus chain W [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.346 (Depositor), 0.341 (DCC)
R-Value Work: 0.281 (Depositor), 0.276 (DCC)
R-Value Observed: 0.284 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.427	α = 90
b = 145.427	β = 90
c = 183.071	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2019-03-06
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description