4RDU | pdb_00004rdu

Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4RDU/pdb
• NAKB: 4RDU

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-09-19 Released: 2014-11-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

To be published.

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: 32.45 kDa 
• Atom Count: 2,393 
• Modeled Residue Count: 178 
• Deposited Residue Count: 186 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein DLX-5	A, D	65	Homo sapiens	Mutation(s): 2  Gene Names: BC006226, DLX5
UniProt & NIH Common Fund Data Resources
Find proteins for P56178 (Homo sapiens) Explore P56178  Go to UniProtKB:  P56178
PHAROS:  P56178 GTEx:  ENSG00000105880

Entity ID: 2
Molecule	Chains	Length	Organism	Image
(DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)	B, C, E, F	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34RDU

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.182	α = 84.13
b = 42.913	β = 77.33
c = 56.104	γ = 67.13

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2023-02-01
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Refinement description