1ALL | pdb_00001all

ALLOPHYCOCYANIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ALL

This is version 1.3 of the entry. See complete history

Literature

Isolation, crystallization, crystal structure analysis and refinement of allophycocyanin from the cyanobacterium Spirulina platensis at 2.3 A resolution.

Brejc, K.Ficner, R.Huber, R.Steinbacher, S.

(1995) J Mol Biology 249: 424-440

  • DOI: https://doi.org/10.1006/jmbi.1995.0307
  • Primary Citation Related Structures: 
    1ALL

  • PubMed Abstract: 

    The phycobiliprotein allophycocyanin from the cyanobacterium Spirulina platensis has been isolated and crystallized. The crystals belong to space group P6(3)22 with cell constants a = b = 101.9 A, c = 130.6 A, alpha = beta = 90 degrees, gamma = 120 degrees, with one (alpha beta) monomer in the asymmetric unit. The three-dimensional structure of the (alpha beta) monomer was solved by multiple isomorphous replacement. The crystal structure has been refined in a cyclic manner by energy-restrained crystallographic refinement and model building. The conventional crystallographic R-factor of the final model is 19.6% with data from 8.0 to 2.3 A. The molecular structure of the subunits resembles other solved phycobiliprotein structures. In comparison to C-phycocyanin and b-phycoerythrin the major differences arise from deletions and insertions of segments involved in the protein-chromophore interactions. The stereochemistry of the alpha 84 and beta 84 chiral atoms are C(2)-R, C(3)-R and C(31)-R. The configuration (C(4)-Z, C(10)-Z and C(15)-Z) and the conformation (C(5)-anti, C(9)-syn and C(14)-anti) are equal for both chromophores.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 35.56 kDa 
  • Atom Count: 2,586 
  • Modeled Residue Count: 321 
  • Deposited Residue Count: 321 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALLOPHYCOCYANIN160Limnospira platensisMutation(s): 0 
UniProt
Find proteins for P72504 (Limnospira platensis)
Explore P72504 
Go to UniProtKB:  P72504
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72504
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ALLOPHYCOCYANIN161Limnospira platensisMutation(s): 0 
UniProt
Find proteins for P72505 (Limnospira platensis)
Explore P72505 
Go to UniProtKB:  P72505
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72505
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC

Query on CYC



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B
L-PEPTIDE LINKINGC5 H10 N2 O3ASN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.9α = 90
b = 101.9β = 90
c = 130.6γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other