2J56

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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: 10.1107/S0909049506051259
  • Primary Citation of Related Structures:  
    2J57, 2J56, 2J55

  • 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 ...

    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.


    Related Citations: 
    • Crystallographic Structures of Methylamine Dehydrogenase Catalytic Intermediates from Paraccocus Denitrificans
      De La Mora-Rey, T., Pearson, A.R., Hoeffner, E., Watts, K.T., Yucel, N., Davidson, V.L., Wilmot, C.M.
      () To be published --: --

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AMICYANINA, B105Paracoccus denitrificansMutation(s): 0 
Gene Names: mauCami
Find proteins for P22364 (Paracoccus denitrificans)
Explore P22364 
Go to UniProtKB:  P22364
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLAMINE DEHYDROGENASE HEAVY CHAINC [auth H], D [auth J]386Paracoccus denitrificansMutation(s): 0 
Gene Names: mauB
EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
Find proteins for P29894 (Paracoccus denitrificans)
Explore P29894 
Go to UniProtKB:  P29894
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLAMINE DEHYDROGENASE LIGHT CHAINE [auth L], F [auth M]131Paracoccus denitrificansMutation(s): 0 
Gene Names: mauA
EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
Find proteins for P22619 (Paracoccus denitrificans)
Explore P22619 
Go to UniProtKB:  P22619
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
G [auth A], H [auth B]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth L], K [auth M]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TQQ
Query on TQQ
E [auth L], F [auth M]L-PEPTIDE LINKINGC11 H11 N3 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.029α = 90
b = 123.029β = 90
c = 245.303γ = 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