1ILX | pdb_00001ilx

Excited State Dynamics in Photosystem II Revised. New Insights from the X-ray Structure.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å

wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

Excited-state dynamics in photosystem II: insights from the x-ray crystal structure.

Vasil'ev, S.Orth, P.Zouni, A.Owens, T.G.Bruce, D.

(2001) Proc Natl Acad Sci U S A 98: 8602-8607

  • DOI: https://doi.org/10.1073/pnas.141239598
  • Primary Citation Related Structures: 
    1ILX

  • PubMed Abstract: 

    The heart of oxygenic photosynthesis is photosystem II (PSII), a multisubunit protein complex that uses solar energy to drive the splitting of water and production of molecular oxygen. The effectiveness of the photochemical reaction center of PSII depends on the efficient transfer of excitation energy from the surrounding antenna chlorophylls. A kinetic model for PSII, based on the x-ray crystal structure coordinates of 37 antenna and reaction center pigment molecules, allows us to map the major energy transfer routes from the antenna chlorophylls to the reaction center chromophores. The model shows that energy transfer to the reaction center is slow compared with the rate of primary electron transport and depends on a few bridging chlorophyll molecules. This unexpected energetic isolation of the reaction center in PSII is similar to that found in the bacterial photosystem, conflicts with the established view of the photophysics of PSII, and may be a functional requirement for primary photochemistry in photosynthesis. In addition, the model predicts a value for the intrinsic photochemical rate constant that is 4 times that found in bacterial reaction centers.


  • Organizational Affiliation
    • Department of Biological Sciences, Brock University, St. Catharines, ON, Canada L2S 3A1. svassili@spartan.ac.brocku.ca

Macromolecule Content 

  • Total Structure Weight: 281.81 kDa 
  • Atom Count: 4,594 
  • Modeled Residue Count: 2,476 
  • Deposited Residue Count: 2,476 
  • Unique protein chains: 9

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBA
A, J
169Synechococcus elongatusMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBD
B, K
174Synechococcus elongatusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBC
C, L
156Synechococcus elongatusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBB
D, M
155Synechococcus elongatusMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBE
E, N
40Synechococcus elongatusMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBF
F, O
30Synechococcus elongatusMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT UNKNOWN
G, P
312Synechococcus elongatusMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBO
H, Q
115Synechococcus elongatusMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM II: SUBUNIT PSBV
I, R
87Synechococcus elongatusMutation(s): 0 

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth D]
AD [auth M]
BA [auth A]
BB [auth D]
AA [auth A],
AB [auth D],
AD [auth M],
BA [auth A],
BB [auth D],
BC [auth L],
BD [auth M],
CB [auth D],
CC [auth L],
DA [auth B],
DB [auth D],
DC [auth L],
DD [auth P],
EB [auth D],
EC [auth L],
FA [auth B],
FB [auth D],
FC [auth L],
GB [auth D],
GC [auth L],
HA [auth C],
HB [auth D],
HC [auth L],
IA [auth C],
IC [auth L],
JA [auth C],
JB [auth G],
JC [auth L],
KA [auth C],
KC [auth L],
LA [auth C],
LC [auth L],
MA [auth C],
MC [auth L],
NA [auth C],
NC [auth M],
OA [auth C],
OC [auth M],
PA [auth C],
PC [auth M],
QA [auth C],
QB [auth J],
QC [auth M],
RA [auth C],
RB [auth J],
RC [auth M],
SA [auth C],
SB [auth J],
SC [auth M],
TA [auth D],
TC [auth M],
UA [auth D],
UB [auth J],
UC [auth M],
VA [auth D],
VB [auth J],
VC [auth M],
W [auth A],
WA [auth D],
WC [auth M],
X [auth A],
XA [auth D],
XB [auth K],
XC [auth M],
Y [auth A],
YA [auth D],
YC [auth M],
ZA [auth D],
ZB [auth K],
ZC [auth M]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
EA [auth B],
TB [auth J],
YB [auth K],
Z [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
AC [auth K],
GA [auth B]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
CD [auth O],
FD [auth R],
IB [auth F],
LB [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CD

Query on CD



Download:Ideal Coordinates CCD File
ED [auth Q],
KB [auth H]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
CA [auth B],
WB [auth K]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
MB [auth J]
NB [auth J]
OB [auth J]
PB [auth J]
S [auth A]
MB [auth J],
NB [auth J],
OB [auth J],
PB [auth J],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.01α = 90
b = 226.72β = 90
c = 308.29γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
DMmodel building
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Non-polymer description