4R5R | pdb_00004r5r

Crystal structure of Rhodostomin KKKRT mutant

• PDB DOI: https://doi.org/10.2210/pdb4R5R/pdb

• Classification: TOXIN
• Organism(s): Calloselasma rhodostoma
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2014-08-21 Released: 2015-08-26 
• Deposition Author(s): Huang, C.H., Shiu, J.H., Chang, Y.T., Jeng, W.Y., Chuang, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.96 Å
• R-Value Free: 
  0.168 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Effects of the regions adjacent to the RGD motif in disintegrins on their inhibitory activities and structures

Huang, C.H., Shiu, J.H., Chang, Y.T., Jeng, W.Y., Chuang, W.J.

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: 14.97 kDa 
• Atom Count: 1,287 
• Modeled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin rhodostomin	A, B	68	Calloselasma rhodostoma	Mutation(s): 5  Gene Names: RHOD
UniProt
Find proteins for P30403 (Calloselasma rhodostoma) Explore P30403  Go to UniProtKB:  P30403

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.96 Å
• R-Value Free:  0.168 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.083	α = 90
b = 79.986	β = 91.3
c = 39.497	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Huang, C.H., Shiu, J.H., Chang, Y.T., Jeng, W.Y., Chuang, W.J.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary