2D5G | pdb_00002d5g

Structure of ubiquitin fold protein R767E mutant

PDB DOI: https://doi.org/10.2210/pdb2D5G/pdb

Classification: SIGNALING PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-11-01 Released: 2006-11-01
Deposition Author(s): Shibata, N., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.314 (Depositor), 0.283 (DCC)
R-Value Work:
0.228 (Depositor), 0.223 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2D5G

This is version 1.4 of the entry. See complete history.

Literature

Structure of ubiquitin fold protein R767E mutant

Shibata, N., Hanamura, T., Yamamoto, R., Ueda, Y., Yamamoto, H., Kikuchi, A., Higuchi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 60.83 kDa
Atom Count: 4,066
Modeled Residue Count: 497
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Axin-1	A, B, C, D, E A, B, C, D, E, F	85	Rattus norvegicus	Mutation(s): 1
UniProt
Find proteins for O70239 (Rattus norvegicus) Explore O70239 Go to UniProtKB: O70239
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O70239
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth E], O [auth F], P [auth F]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.314 (Depositor), 0.283 (DCC)
R-Value Work: 0.228 (Depositor), 0.223 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.55	α = 90
b = 125.55	β = 90
c = 115.43	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-11-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2024-05-29
Changes: Data collection

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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.