7DJY | pdb_00007djy

Clec4f Nanobody 322

PDB DOI: https://doi.org/10.2210/pdb7DJY/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Lamium maculatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-11-22 Released: 2021-11-24
Deposition Author(s): Wen, Y., Zheng, F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.266 (Depositor), 0.270 (DCC)
R-Value Work:
0.228 (Depositor), 0.240 (DCC)
R-Value Observed:
0.232 (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

Clec4f Nanobody 322

Wen, Y., Zheng, F.

To be published.

Macromolecule Content

Total Structure Weight: 55.62 kDa
Atom Count: 3,729
Modeled Residue Count: 491
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clec4f Nanobody 322	A, B, C, D	129	Lamium maculatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.266 (Depositor), 0.270 (DCC)
R-Value Work: 0.228 (Depositor), 0.240 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.469	α = 90
b = 80.469	β = 90
c = 107.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-11-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870132, 82072237

Revision History (Full details and data files)

Version 1.0: 2021-11-24
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.