2J57

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry.

Pearson, A.R., Pahl, R., Kovaleva, E.G., Davidson, V.L., Wilmot, C.M.

(2007) J Synchrotron Radiat 14: 92

  • DOI: https://doi.org/10.1107/S0909049506051259
  • Primary Citation of Related Structures:  
    2J55, 2J56, 2J57

  • PubMed Abstract: 

    X-ray exposure during crystallographic data collection can result in unintended redox changes in proteins containing functionally important redox centers. In order to directly monitor X-ray-derived redox changes in trapped oxidative half-reaction intermediates of Paracoccus denitrificans methylamine dehydrogenase, a commercially available single-crystal UV/Vis microspectrophotometer was installed on-line at the BioCARS beamline 14-BM-C at the Advanced Photon Source, Argonne, USA. Monitoring the redox state of the intermediates during X-ray exposure permitted the creation of a general multi-crystal data collection strategy to generate true structures of each redox intermediate.

    • Organizational Affiliation: 

    Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, MN 55455, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMICYANIN
A, B, C, D
105Paracoccus denitrificansMutation(s): 0 
UniProt
Find proteins for P22364 (Paracoccus denitrificans)
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Go to UniProtKB:  P22364
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22364
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
METHYLAMINE DEHYDROGENASE HEAVY CHAINE [auth G],
F [auth H],
G [auth I],
H [auth J]		386Paracoccus denitrificansMutation(s): 0 
EC: 1.4.99.3
UniProt
Find proteins for P29894 (Paracoccus denitrificans)
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UniProt GroupP29894
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
METHYLAMINE DEHYDROGENASE LIGHT CHAINI [auth K],
J [auth L],
K [auth M],
L [auth N]		131Paracoccus denitrificansMutation(s): 0 
EC: 1.4.99.3
UniProt
Find proteins for P22619 (Paracoccus denitrificans)
Explore P22619 
Go to UniProtKB:  P22619
Entity Groups  
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UniProt GroupP22619
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TQQ
Query on TQQ		I [auth K],
J [auth L],
K [auth M],
L [auth N]		L-PEPTIDE LINKINGC11 H11 N3 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.131α = 90
b = 123.439β = 90
c = 246.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance