3RCO | pdb_00003rco

Crystal structure of a conserved motif in human TDRD7

PDB DOI: https://doi.org/10.2210/pdb3RCO/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-03-31 Released: 2012-04-04
Deposition Author(s): Dong, A., Xu, C., Walker, J.R., Lam, R., Guo, Y., Bian, C., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.174 (Depositor), 0.172 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3RCO

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

Literature

Crystal structure of a conserved motif in human TDRD7

Xu, C., Dong, A., Walker, J.R., Lam, R., Guo, Y., Bian, C., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 20.37 kDa
Atom Count: 1,407
Modeled Residue Count: 154
Deposited Residue Count: 178
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tudor domain-containing protein 7	A, B	89	Homo sapiens	Mutation(s): 0 Gene Names: TDRD7, PCTAIRE2BP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHU6 (Homo sapiens) Explore Q8NHU6 Go to UniProtKB: Q8NHU6
PHAROS: Q8NHU6 GTEx: ENSG00000196116
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NHU6
Sequence Annotations Expand
Reference Sequence

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 M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] 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 M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] 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 M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] 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], K [auth B], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		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] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [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] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.174 (Depositor), 0.172 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.788	α = 90
b = 99.788	β = 90
c = 99.788	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SOLVE	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations