8T29

Crystal structure of SCV PTE RNA in complex with Fab BL3-6

PDB DOI: https://doi.org/10.2210/pdb8T29/pdb
NAKB: 8T29

Classification: RNA/IMMUNE SYSTEM
Organism(s): Saguaro cactus virus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-06-05 Released: 2024-01-10
Deposition Author(s): Ojha, M., Koirala, D.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free: 0.233
R-Value Work: 0.179
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of SCV PTE RNA in complex with Fab BL3-6

Ojha, M., Koirala, D.

To be published.

Macromolecule Content

Total Structure Weight: 77.33 kDa
Atom Count: 5,223
Modelled Residue Count: 525
Deposited Residue Count: 538
Unique protein chains: 2
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
BL3-6 Fab heavy chain	B [auth A]	233	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab light chain	C [auth B]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (90-MER)	A [auth R]	90	Saguaro cactus virus
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free: 0.233
R-Value Work: 0.179
R-Value Observed: 0.185
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.437	α = 90
b = 81.188	β = 90
c = 321.188	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	United States	NA

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.