3D38

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device.

Li, L.Nachtergaele, S.Seddon, A.M.Tereshko, V.Ponomarenko, N.Ismagilov, R.F.

(2008) J Am Chem Soc 130: 14324-14328

  • DOI: https://doi.org/10.1021/ja805361j
  • Primary Citation of Related Structures:  
    3D38

  • PubMed Abstract: 

    This paper utilizes cyclodextrin-based host-guest chemistry in a microfluidic device to modulate the crystallization of membrane proteins and the process of concentration of membrane protein samples. Methyl-beta-cyclodextrin (MBCD) can efficiently capture a wide variety of detergents commonly used for the stabilization of membrane proteins by sequestering detergent monomers. Reaction Center (RC) from Blastochloris viridis was used here as a model system. In the process of concentrating membrane protein samples, MBCD was shown to break up free detergent micelles and prevent them from being concentrated. The addition of an optimal amount of MBCD to the RC sample captured loosely bound detergent from the protein-detergent complex and improved sample homogeneity, as characterized by dynamic light scattering. Using plug-based microfluidics, RC crystals were grown in the presence of MBCD, giving a different morphology and space group than crystals grown without MBCD. The crystal structure of RC crystallized in the presence of MBCD was consistent with the changes in packing and crystal contacts hypothesized for removal of loosely bound detergent. The incorporation of MBCD into a plug-based microfluidic crystallization method allows efficient use of limited membrane protein sample by reducing the amount of protein required and combining sparse matrix screening and optimization in one experiment. The use of MBCD for detergent capture can be expanded to develop cyclodextrin-derived molecules for fine-tuned detergent capture and thus modulate membrane protein crystallization in an even more controllable way.


  • Organizational Affiliation

    Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]336Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07173 (Blastochloris viridis)
Explore P07173 
Go to UniProtKB:  P07173
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07173
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein H chainB [auth H]258Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06008 (Blastochloris viridis)
Explore P06008 
Go to UniProtKB:  P06008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06008
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainC [auth L]273Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06009 (Blastochloris viridis)
Explore P06009 
Go to UniProtKB:  P06009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06009
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainD [auth M]323Blastochloris viridisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06010 (Blastochloris viridis)
Explore P06010 
Go to UniProtKB:  P06010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06010
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCB
Query on BCB

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KA [auth M],
LA [auth M],
Y [auth L],
Z [auth L]
BACTERIOCHLOROPHYLL B
C55 H72 Mg N4 O6
QNWPCDKNPGOYNP-DSENBSCCSA-M
BPB
Query on BPB

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AA [auth L],
MA [auth M]
BACTERIOPHEOPHYTIN B
C55 H74 N4 O6
SFKCKJXMIAKQMY-GTTFDWDMSA-N
MQ9
Query on MQ9

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JA [auth M]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
HEC
Query on HEC

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L [auth C],
M [auth C],
N [auth C],
O [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
NS5
Query on NS5

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NA [auth M]15-cis-1,2-dihydroneurosporene
C40 H60
NHKJSVKSSGKUCH-DBWJSHEJSA-N
UQ1
Query on UQ1

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BA [auth L],
CA [auth L]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
LDA
Query on LDA

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DA [auth L],
OA [auth M],
V [auth H],
W [auth H]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
HTO
Query on HTO

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P [auth C],
Q [auth C],
X [auth H]
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
SO4
Query on SO4

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E [auth C]
F [auth C]
FA [auth M]
G [auth C]
GA [auth M]
E [auth C],
F [auth C],
FA [auth M],
G [auth C],
GA [auth M],
H [auth C],
HA [auth M],
I [auth C],
IA [auth M],
J [auth C],
K [auth C],
R [auth H],
S [auth H],
T [auth H],
U [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE2
Query on FE2

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EA [auth M]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
B [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 241.171α = 90
b = 241.171β = 90
c = 113.391γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description