2R9U | pdb_00002r9u

Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain

PDB DOI: https://doi.org/10.2210/pdb2R9U/pdb

Classification: IMMUNE SYSTEM
Organism(s): Petromyzon marinus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2007-09-13 Released: 2009-03-10
Deposition Author(s): Han, B.W., Herrin, B.R., Choe, J., Cooper, M.D., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.264 (Depositor), 0.270 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain.

Han, B.W., Herrin, B.R., Morris, G.M., Choe, J., Cooper, M.D., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 77.96 kDa
Atom Count: 5,831
Modeled Residue Count: 696
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable lymphocyte receptor	A, B, C, D	174	Petromyzon marinus	Mutation(s): 0
UniProt
Find proteins for Q6E4B4 (Petromyzon marinus) Explore Q6E4B4 Go to UniProtKB: Q6E4B4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6E4B4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.264 (Depositor), 0.270 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.109	α = 90
b = 61.057	β = 107.35
c = 98.081	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
CaspR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

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.