2VSV

Crystal structure of the PDZ domain of human rhophilin-2

• PDB DOI: https://doi.org/10.2210/pdb2VSV/pdb

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


• Deposited: 2008-04-29 Released: 2008-07-15 
• Deposition Author(s): Pike, A.C.W., Kochan, G., Sun, Z., Shafqat, N., Pilka, E.S., Roos, A., Elkins, J., Burgess-Brown, N., Murray, J.W., von Delft, F., Wikstrom, M., Edwards, A., Arrowsmith, C.H., Bountra, C., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of the Pdz Domain of Human Rhophilin-2

Pike, A.C.W., Kochan, G., Sun, Z., Shafqat, N., Pilka, E.S., Roos, A., Elkins, J., Burgess-Brown, N., Murray, J.W., von Delft, F., Wikstrom, M., Edwards, A., Arrowsmith, C.H., Bountra, C., Oppermann, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.56 kDa 
• Atom Count: 1,639 
• Modelled Residue Count: 201 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHOPHILIN-2	A, B	109	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUC4 (Homo sapiens) Explore Q8IUC4  Go to UniProtKB:  Q8IUC4
PHAROS:  Q8IUC4 GTEx:  ENSG00000131941

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.25	α = 90
b = 39.89	β = 115.78
c = 73.48	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: 2008-07-15 
Deposition Author(s): Pike, A.C.W., Kochan, G., Sun, Z., Shafqat, N., Pilka, E.S., Roos, A., Elkins, J., Burgess-Brown, N., Murray, J.W., von Delft, F., Wikstrom, M., Edwards, A., Arrowsmith, C.H., Bountra, C., Oppermann, U.

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description