1NKZ

Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.8 of the entry. See complete history


Literature

The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 A resolution and 100K : new structural features and functionally relevant motions.

Papiz, M.Z.Prince, S.M.Howard, T.Cogdell, R.J.Isaacs, N.W.

(2003) J Mol Biol 326: 1523-1538

  • DOI: https://doi.org/10.1016/s0022-2836(03)00024-x
  • Primary Citation of Related Structures:  
    1NKZ

  • PubMed Abstract: 

    The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.


  • Organizational Affiliation

    Department of Synchrotron Radiation, CCLRC Daresbury Laboratory, Keckwick Lane, Warrington, Cheshire WA4 4AD, UK. m.papiz@dl.ac.uk


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850, alpha chain
A, C, E
53Rhodoblastus acidophilusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P26789 (Rhodoblastus acidophilus)
Explore P26789 
Go to UniProtKB:  P26789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26789
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein B-800/850, beta chain
B, D, F
41Rhodoblastus acidophilusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26790 (Rhodoblastus acidophilus)
Explore P26790 
Go to UniProtKB:  P26790
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26790
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL
Query on BCL

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
I [auth A]
J [auth A]
L [auth B]
AA [auth E],
DA [auth F],
I [auth A],
J [auth A],
L [auth B],
Q [auth C],
R [auth C],
U [auth D],
Z [auth E]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
RG1
Query on RG1

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G [auth A]
K [auth B]
M [auth C]
N [auth C]
T [auth D]
G [auth A],
K [auth B],
M [auth C],
N [auth C],
T [auth D],
V [auth E]
Rhodopin b-D-glucoside
C46 H66 O6
ISHBHDBCVQRMDY-GZIKAPSJSA-N
BOG
Query on BOG

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H [auth A]
O [auth C]
P [auth C]
W [auth E]
X [auth E]
H [auth A],
O [auth C],
P [auth C],
W [auth E],
X [auth E],
Y [auth E]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
BEN
Query on BEN

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BA [auth E],
CA [auth E],
S [auth C]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
A, C, E
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.052α = 90
b = 117.052β = 90
c = 298.438γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
DMmodel building
REFMACrefinement
CCP4data scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2014-04-16
    Changes: Data collection
  • Version 1.4: 2016-03-30
    Changes: Non-polymer description
  • Version 1.5: 2017-02-01
    Changes: Structure summary
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.7: 2023-08-16
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 1.8: 2024-03-13
    Changes: Data collection, Source and taxonomy