4W8H | pdb_00004w8h

Crystal structure of the TIR domain of the Toll-related Receptor TRR-2 from the lower metazoan Hydra magnipapillata (crystal form II)

PDB DOI: https://doi.org/10.2210/pdb4W8H/pdb

Classification: SIGNALING PROTEIN
Organism(s): Hydra vulgaris, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-24 Released: 2015-09-09
Deposition Author(s): Weisse, R.H.-J., Scheidig, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free:
0.171 (Depositor), 0.174 (DCC)
R-Value Work:
0.140 (Depositor), 0.146 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the TIR domain of the Toll-related Receptor TRR-2 from the lower metazoan Hydra magnipapillata (crystal form II)

Weisse, R.H.-J., Scheidig, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 16.21 kDa
Atom Count: 1,314
Modeled Residue Count: 131
Deposited Residue Count: 135
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-receptor-related 2	A	129	Hydra vulgaris	Mutation(s): 0 Gene Names: TRR-2
UniProt
Find proteins for A6M946 (Hydra vulgaris) Explore A6M946 Go to UniProtKB: A6M946
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6M946
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hexa-His tag	B [auth D]	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.171 (Depositor), 0.174 (DCC)
R-Value Work: 0.140 (Depositor), 0.146 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.73	α = 90
b = 63.57	β = 105.17
c = 32.12	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Weisse, R.H.-J.

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.