4RGH

Human DNA Damage-Inducible Protein: From Protein Chemistry and 3D Structure to Deciphering its Cellular Role

• PDB DOI: https://doi.org/10.2210/pdb4RGH/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-30 Released: 2016-02-17 
• Deposition Author(s): Brynda, J., Grantz Saskova, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Human DNA Damage-Inducible Protein: From Protein Chemistry and 3D Structure to Deciphering its Cellular Role

Siva, M., Svoboda, M., Veverka, V., Brynda, J., Trempe, J.-F., Kozisek, M., Fleisigova, I., Belza, J., Konvalinka, J., Grantz Saskova, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 38.1 kDa 
• Atom Count: 2,032 
• Modelled Residue Count: 248 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein DDI1 homolog 2	A, B	169	Homo sapiens	Mutation(s): 0  Gene Names: DDI2
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TDH0 (Homo sapiens) Explore Q5TDH0  Go to UniProtKB:  Q5TDH0
PHAROS:  Q5TDH0 GTEx:  ENSG00000197312

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.87	α = 90
b = 86.4	β = 90
c = 52.12	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Brynda, J., Grantz Saskova, K.

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description