3GIX | pdb_00003gix

Crystal structure of human splicing factor dim2

PDB DOI: https://doi.org/10.2210/pdb3GIX/pdb

Classification: SPLICING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-06 Released: 2010-03-16
Deposition Author(s): Jin, T.C., Guo, F., Zhang, Y.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free:
0.197 (Depositor)
R-Value Work:
0.145 (Depositor), 0.142 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3GIX

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of human splicing factor dim2

Jin, T.C., Guo, F., Wang, Y.T., Howard, A., Zhang, Y.Z.

To be published.

Macromolecule Content

Total Structure Weight: 34.26 kDa
Atom Count: 2,861
Modeled Residue Count: 282
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-like protein 4B	A, B	149	Homo sapiens	Mutation(s): 0 Gene Names: DIM2, DLP, TXNL4B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX01 (Homo sapiens) Explore Q9NX01 Go to UniProtKB: Q9NX01
PHAROS: Q9NX01 GTEx: ENSG00000140830
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NX01
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.197 (Depositor)
R-Value Work: 0.145 (Depositor), 0.142 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.325	α = 90
b = 63.64	β = 92.29
c = 51.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-06
Changes: Advisory, Data collection, Database references, Refinement description, 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.