3QHB | pdb_00003qhb

Crystal structure of oxidized Symerythrin from Cyanophora paradoxa

• PDB DOI: https://doi.org/10.2210/pdb3QHB/pdb

• Classification: METAL TRANSPORT
• Organism(s): Cyanophora paradoxa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-25 Released: 2011-05-25 
• Deposition Author(s): Cooley, R.B., Arp, D.J., Karplus, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.125 (Depositor), 0.120 (DCC) 
• R-Value Work: 
  0.101 (Depositor), 0.100 (DCC) 
• R-Value Observed: 
  0.102 (Depositor) 

Starting Model: experimental

Literature

A diiron protein autogenerates a valine-phenylalanine cross-link.

Cooley, R.B., Rhoads, T.W., Arp, D.J., Karplus, P.A.

(2011) Science 332: 929-929

• PubMed: 21596985 
• DOI: https://doi.org/10.1126/science.1205687
• Primary Citation of Related Structures:  
  3QHB


• PubMed Abstract: 
  

  All known internal covalent cross-links in proteins involve functionalized groups having oxygen, nitrogen, or sulfur atoms present to facilitate their formation. Here, we report a carbon-carbon cross-link between two unfunctionalized side chains. This valine-phenyalanine cross-link, produced in an oxygen-dependent reaction, is generated by its own carboxylate-bridged diiron center and serves to stabilize the metallocenter. This finding opens the door to new types of posttranslational modifications, and it demonstrates new catalytic potential of diiron centers.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA.

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: 39.99 kDa 
• Atom Count: 3,534 
• Modeled Residue Count: 358 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Symerythrin	A, B	179	Cyanophora paradoxa	Mutation(s): 0  Gene Names: ORF180
UniProt
Find proteins for P48329 (Cyanophora paradoxa) Explore P48329  Go to UniProtKB:  P48329

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth A], E [auth B], F [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.125 (Depositor), 0.120 (DCC) 
• R-Value Work:  0.101 (Depositor), 0.100 (DCC) 
• R-Value Observed: 0.102 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.593	α = 90
b = 81.593	β = 90
c = 46.277	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Cooley, R.B., Arp, D.J., Karplus, P.A.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary