3S93 | pdb_00003s93

Crystal structure of conserved motif in TDRD5

PDB DOI: https://doi.org/10.2210/pdb3S93/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-05-31 Released: 2011-08-31
Deposition Author(s): Chao, X., Tempel, W., Bian, C., Kania, J., Wernimont, A.K., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.271 (Depositor), 0.261 (DCC)
R-Value Work:
0.245 (Depositor), 0.257 (DCC)
R-Value Observed:
0.246 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3S93

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

Literature

Crystal structure of conserved motif in TDRD5

Chao, X., Tempel, W., Bian, C., Kania, J., Wernimont, A.K., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Macromolecule Content

Total Structure Weight: 22.72 kDa
Atom Count: 1,238
Modeled Residue Count: 161
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tudor domain-containing protein 5	A, B	102	Homo sapiens	Mutation(s): 0 Gene Names: TDRD5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT2 (Homo sapiens) Explore Q8NAT2 Go to UniProtKB: Q8NAT2
PHAROS: Q8NAT2 GTEx: ENSG00000162782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NAT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.271 (Depositor), 0.261 (DCC)
R-Value Work: 0.245 (Depositor), 0.257 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.94	α = 90
b = 43.33	β = 90
c = 126.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SOLVE	phasing
RESOLVE	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Wernimont, A.K.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references

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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.