6JRI | pdb_00006jri

Crystal structure of Nanobody

PDB DOI: https://doi.org/10.2210/pdb6JRI/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Vicugna pacos
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-04 Released: 2020-05-06
Deposition Author(s): Mo, X., Li, J., Xu, X., Yuan, A.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.259 (Depositor), 0.267 (DCC)
R-Value Work:
0.235 (Depositor), 0.241 (DCC)
R-Value Observed:
0.237 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of nanobody at 3.1 Angstroms resolution.

Mo, X.

To be published.

Macromolecule Content

Total Structure Weight: 114.49 kDa
Atom Count: 7,700
Modeled Residue Count: 989
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	A [auth B] B [auth A] C D E A [auth B], B [auth A], C, D, E, F, G, H	130	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.259 (Depositor), 0.267 (DCC)
R-Value Work: 0.235 (Depositor), 0.241 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.305	α = 90
b = 85.471	β = 91.05
c = 229.145	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Structure summary

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.