1JGY | pdb_00001jgy

Photosynthetic Reaction Center Mutant With Tyr M 76 Replaced With Phe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.257 (Depositor) 
  • R-Value Work: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1JGY

This is version 1.4 of the entry. See complete history

Literature

Individual interactions influence the crystalline order for membrane proteins.

Camara-Artigas, A.Magee, C.L.Williams, J.C.Allen, J.P.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1281-1286

  • DOI: https://doi.org/10.1107/s090744490101109x
  • Primary Citation Related Structures: 
    1JGW, 1JGX, 1JGY, 1JGZ, 1JH0

  • PubMed Abstract: 

    The role of contact interactions in the crystallization of membrane proteins was assessed by mutation of amino-acid residues on the surface of the reaction center from Rhodobacter sphaeroides. Five single-site mutants were constructed, with changes in contact regions found in the trigonal and tetragonal forms but not the orthorhombic form. Crystallization trials for the tetragonal form yielded either no crystals or crystals with an altered morphology, whereas crystals grew in the other two forms, indicating that these interactions are essential for the stability of the tetragonal crystals. Changes in the structures determined by X-ray diffraction of trigonal crystals for each mutant were related to the quality of the diffraction. Significant differences in the resolution limit of the crystals were associated with the loss of specific interactions between neighboring proteins. The results suggest that the contact regions are crucial for obtaining highly ordered crystals of membrane proteins.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA.

Macromolecule Content 

  • Total Structure Weight: 102.17 kDa 
  • Atom Count: 7,123 
  • Modeled Residue Count: 823 
  • Deposited Residue Count: 848 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic Reaction Center L SubunitA [auth L]281Cereibacter sphaeroidesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides)
Explore P0C0Y8 
Go to UniProtKB:  P0C0Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic Reaction Center M SubunitB [auth M]307Cereibacter sphaeroidesMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides)
Explore P0C0Y9 
Go to UniProtKB:  P0C0Y9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic Reaction Center H SubunitC [auth H]260Cereibacter sphaeroidesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides)
Explore P0C0Y7 
Go to UniProtKB:  P0C0Y7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0Y7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
M
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL

Query on BCL



Download:Ideal Coordinates CCD File
D [auth L],
E [auth L],
H [auth M],
I [auth M]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
F [auth L],
J [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10

Query on U10



Download:Ideal Coordinates CCD File
K [auth M]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
SPO

Query on SPO



Download:Ideal Coordinates CCD File
L [auth M]SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
G [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.257 (Depositor) 
  • R-Value Work:  0.218 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.68α = 90
b = 141.68β = 90
c = 186.84γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description