3V71 | pdb_00003v71

Crystal structure of PUF-6 in complex with 5BE13 RNA

PDB DOI: https://doi.org/10.2210/pdb3V71/pdb
NAKB: 3V71

Classification: RNA binding protein/RNA
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-20 Released: 2012-01-04
Deposition Author(s): Qiu, C., Kershner, A., Wang, Y., Holley, C.H., Wilinski, D., Keles, S., Kimble, J., Wickens, M., Hall, T.M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.241 (Depositor), 0.234 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Divergence of PUF protein specificity through variations in an RNA-binding pocket

Qiu, C., Kershner, A., Wang, Y., Holley, C.H., Wilinski, D., Keles, S., Kimble, J., Wickens, M., Hall, T.M.T.

(2012) J Biol Chem

Macromolecule Content

Total Structure Weight: 47.97 kDa
Atom Count: 3,089
Modeled Residue Count: 371
Deposited Residue Count: 395
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Puf (Pumilio/fbf) domain-containing protein 7, confirmed by transcript evidence	A	382	Caenorhabditis elegans	Mutation(s): 0 Gene Names: puf-7, B0273.2
UniProt
Find proteins for O44169 (Caenorhabditis elegans) Explore O44169 Go to UniProtKB: O44169
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O44169
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(CPUPCPUPGPUPAPUPCPUPUPGP*U)-3')	B	13	Caenorhabditis elegans
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.241 (Depositor), 0.234 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.806	α = 90
b = 87.836	β = 90
c = 129.782	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-01-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-04
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description