1M2T

Mistletoe Lectin I from Viscum album in Complex with Adenine Monophosphate. Crystal Structure at 1.9 A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystallisation under microgravity of mistletoe lectin I from Viscum album with adenine monophosphate and the crystal structure at 1.9 A resolution.

Krauspenhaar, R.Rypniewski, W.Kalkura, N.Moore, K.DeLucas, L.Stoeva, S.Mikhailov, A.Voelter, W.Betzel, C.h.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1704-1707

  • DOI: https://doi.org/10.1107/s0907444902014270
  • Primary Citation of Related Structures:  
    1M2T

  • PubMed Abstract: 

    The crystal structure of the ribosome-inactivating protein (RIP) mistletoe lectin I (ML-I) from Viscum album in complex with adenine has been refined to 1.9 A resolution. High quality crystals of the ML-I complex were obtained by the method of vapour diffusion using the high density protein crystal growth system (HDPCG) on the international space station, mission ISS 6A. Hexagonal crystals were grown during three months under microgravity conditions. Diffraction data to 1.9A were collected applying synchrotron radiation and cryo- techniques. The structure was refined subsequently to analyse the structure of ML-I and particularly the active site conformation, complexed by adenine that mimics the RNA substrate binding.


  • Organizational Affiliation

    Institute of Medical Biochemistry and Molecular Biology, University Hospital, c/o DESY, Build 22a, Notkestr 85, 22603 Hamburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mistletoe lectin I A chain254Viscum albumMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P81446 (Viscum album)
Explore P81446 
Go to UniProtKB:  P81446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81446
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mistletoe lectin I B chain263Viscum albumMutation(s): 0 
UniProt
Find proteins for P81446 (Viscum album)
Explore P81446 
Go to UniProtKB:  P81446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81446
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]
E [auth A]
K [auth B]
M [auth B]
N [auth B]
C [auth A],
E [auth A],
K [auth B],
M [auth B],
N [auth B],
O [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
ADE
Query on ADE

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F [auth A]ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
P [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.12α = 90
b = 107.12β = 90
c = 309.82γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-20
    Changes: Structure summary