3QJJ

One RAMP protein binding different RNA substrates

PDB DOI: https://doi.org/10.2210/pdb3QJJ/pdb
NAKB: 3QJJ

Classification: IMMUNE SYSTEM/RNA
Organism(s): Pyrococcus horikoshii
Mutation(s): No

Deposited: 2011-01-29 Released: 2012-02-08
Deposition Author(s): Wang, R., Zheng, H., Preamplume, G., Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.262
R-Value Work: 0.211
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

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

Literature

Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA

Wang, R., Zheng, H., Preamplume, G., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 63.86 kDa
Atom Count: 4,436
Modelled Residue Count: 507
Deposited Residue Count: 510
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0350	B [auth A], C [auth B]	243	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH0350
UniProt
Find proteins for O58088 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58088 Go to UniProtKB: O58088
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58088
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(GPUPUPGPAPAPAPUPCPAPGPA)-3')	A [auth R], D [auth Q]	12	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.262
R-Value Work: 0.211
R-Value Observed: 0.216
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.269	α = 90
b = 75.269	β = 90
c = 257.351	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.