4LCZ

Crystal structure of a multilayer-packed major light-harvesting complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Crystal structure of a multilayer packed major light-harvesting complex: implications for grana stacking in higher plants.

Wan, T.Li, M.Zhao, X.Zhang, J.Liu, Z.Chang, W.

(2014) Mol Plant 7: 916-919

  • DOI: https://doi.org/10.1093/mp/ssu005
  • Primary Citation of Related Structures:  
    4LCZ

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15th Datun Road, Chaoyang District, Beijing, 100101, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major chlorophyll a/b binding protein LHCb1.3
A, B, C
224Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12333 (Spinacia oleracea)
Explore P12333 
Go to UniProtKB:  P12333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12333
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL
Query on CHL

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DA [auth B]
DB [auth C]
EB [auth C]
FB [auth C]
GB [auth C]
DA [auth B],
DB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
H [auth A],
HA [auth B],
HB [auth C],
IA [auth B],
JA [auth B],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
ZA [auth C]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AB [auth C]
BB [auth C]
CB [auth C]
EA [auth B]
FA [auth B]
AB [auth C],
BB [auth C],
CB [auth C],
EA [auth B],
FA [auth B],
GA [auth B],
I [auth A],
IB [auth C],
J [auth A],
JB [auth C],
K [auth A],
KB [auth C],
LB [auth C],
MA [auth B],
MB [auth C],
NA [auth B],
OA [auth B],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG
Query on LHG

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CA [auth B],
G [auth A],
YA [auth C]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

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BA [auth B],
F [auth A],
XA [auth C]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
LUT
Query on LUT

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AA [auth B]
D [auth A]
E [auth A]
VA [auth C]
WA [auth C]
AA [auth B],
D [auth A],
E [auth A],
VA [auth C],
WA [auth C],
Z [auth B]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
CAC
Query on CAC

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NB [auth C],
RA [auth B],
V [auth A]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN
Query on ZN

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PB [auth C],
TA [auth B],
W [auth A],
X [auth A],
Y [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

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OB [auth C],
QB [auth C],
RB [auth C],
SA [auth B],
UA [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.195α = 90
b = 115.097β = 113.23
c = 109.597γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Advisory, Data collection
  • Version 2.0: 2022-08-24
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Refinement description