4Q5W | pdb_00004q5w

Crystal structure of extended-Tudor 9 of Drosophila melanogaster

• PDB DOI: https://doi.org/10.2210/pdb4Q5W/pdb

• Classification: TRANSCRIPTION
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-17 Released: 2014-05-21 
• Deposition Author(s): Ren, R., Liu, H., Wang, W., Wang, M., Yang, N., Dong, Y., Gong, W., Lehmann, R., Xu, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structure and domain organization of Drosophila Tudor

Ren, R., Liu, H., Wang, W., Wang, M., Yang, N., Dong, Y.H., Gong, W., Lehmann, R., Xu, R.M.

(2014) Cell Res 24: 1146-1149

• PubMed: 24810300 
• DOI: https://doi.org/10.1038/cr.2014.63
• Primary Citation Related Structures: 
  4Q5W, 4Q5Y

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Organizational Affiliation: 
• 1] National Laboratory of Biomacromolecules, National Center for Protein Science (Beijing), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China.
1] National Laboratory of Biomacromolecules, National Center for Protein Science (Beijing), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] Current address: Tianjin Institute of Industrial Biology, Chinese Academy of Sciences, Tianjin 300308, China.
Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
National Laboratory of Biomacromolecules, National Center for Protein Science (Beijing), Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Skirball Institute of Biomolecular Medicine, HHMI, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.82 kDa 
• Atom Count: 3,494 
• Modeled Residue Count: 363 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal protein tudor	A, B	183	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG9450, tud, tudor
UniProt
Find proteins for P25823 (Drosophila melanogaster) Explore P25823  Go to UniProtKB:  P25823

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.23	α = 90
b = 105.678	β = 100.57
c = 52.603	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Ren, R., Liu, H., Wang, W., Wang, M., Yang, N., Dong, Y., Gong, W., Lehmann, R., Xu, R.M.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations