1V2B

Crystal Structure of PsbP Protein in the Oxygen-Evolving Complex of Photosystem II from Higher Plants


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Literature

Crystal structure of the PsbP protein of photosystem II from Nicotiana tabacum

Ifuku, K.Nakatsu, T.Kato, H.Sato, F.

(2004) EMBO Rep 5: 362-367

  • DOI: 10.1038/sj.embor.7400113
  • Primary Citation of Related Structures:  
    1V2B

  • PubMed Abstract: 
  • PsbP is a membrane-extrinsic subunit of the water-oxidizing complex photosystem II (PS II). The evolutionary origin of PsbP has long been a mystery because it specifically exists in higher plants and green algae but not in cyanobacteria. We report here the crystal structure of PsbP from Nicotiana tabacum at a resolution of 1 ...

    PsbP is a membrane-extrinsic subunit of the water-oxidizing complex photosystem II (PS II). The evolutionary origin of PsbP has long been a mystery because it specifically exists in higher plants and green algae but not in cyanobacteria. We report here the crystal structure of PsbP from Nicotiana tabacum at a resolution of 1.6 A. Its structure is mainly composed of beta-sheet, and is not similar to any structures in cyanobacterial PS II. However, the electrostatic surface potential of PsbP is similar to that of cyanobacterial PsbV (cyt c(550)), which has a function similar to PsbP. A structural homology search with the DALI algorithm indicated that the folding of PsbP is very similar to that of Mog1p, a regulatory protein for the nuclear transport of Ran GTPase. The structure of PsbP provides insight into its novel function in GTP-regulated metabolism in PS II.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies on the extrinsic 23 kDa protein in the oxygen-evolving complex of photosystem II
      Ifuku, K., Nakatsu, T., Kato, H., Sato, F.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 1462
    • A Truncated Mutant of the Extrinsic 23-kDa Protein that Absolutely Requires the Extrinsic 17-kDa Protein for Ca2+ Retention in Photosystem II
      Ifuku, K., Sato, F.
      (2002) Plant Cell Physiol 43: 1244
    • Importance of the N-terminal Sequence of the Extrinsic 23 kDa Polypeptide in Photosystem II in Oxygen Evolution
      Ifuku, K., Sato, F.
      (2001) Biochim Biophys Acta 1546: 196

    Organizational Affiliation

    Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
23-kDa polypeptide of photosystem II oxygen-evolving complexA, B177Nicotiana tabacumMutation(s): 0 
Gene Names: PSBPPSBP2OEE2-B
UniProt
Find proteins for P18212 (Nicotiana tabacum)
Explore P18212 
Go to UniProtKB:  P18212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18212
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.52α = 90
b = 90.442β = 90
c = 52.635γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary