2OXC | pdb_00002oxc

Human DEAD-box RNA helicase DDX20, DEAD domain in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb2OXC/pdb

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


• Deposited: 2007-02-20 Released: 2007-02-27 
• Deposition Author(s): Karlberg, T., Ogg, D., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.175 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Human DEAD-box RNA helicase DDX20

Karlberg, T., Ogg, D., H Arrowsmith, C., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.21 kDa 
• Atom Count: 3,949 
• Modeled Residue Count: 410 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX20	A, B	230	Homo sapiens	Mutation(s): 0  Gene Names: DDX20, DP103, GEMIN3 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt), 3.6.1.15 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI6 (Homo sapiens) Explore Q9UHI6  Go to UniProtKB:  Q9UHI6
PHAROS:  Q9UHI6 GTEx:  ENSG00000064703

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.175 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.8	α = 90
b = 63.8	β = 90
c = 214.3	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Karlberg, T., Ogg, D., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description