6G8W | pdb_00006g8w

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130

• PDB DOI: https://doi.org/10.2210/pdb6G8W/pdb

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


• Deposited: 2018-04-10 Released: 2019-04-24 
• Deposition Author(s): Jurk, C.M., Roske, Y., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130

Jurk, C.M., Roske, Y., Heinemann, U.

(2018) Croat Chem Acta 

• DOI: https://doi.org/10.5562/cca3341

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.48 kDa 
• Atom Count: 1,494 
• Modeled Residue Count: 179 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi reassembly-stacking protein 1	A, B	97	Homo sapiens	Mutation(s): 0  Gene Names: GORASP1, GOLPH5, GRASP65
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQQ3 (Homo sapiens) Explore Q9BQQ3  Go to UniProtKB:  Q9BQQ3
PHAROS:  Q9BQQ3 GTEx:  ENSG00000114745

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.825	α = 90
b = 82.613	β = 110.82
c = 49.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Jurk, C.M., Roske, Y., Heinemann, U.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description