2E39

Crystal structure of the CN-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

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This is version 2.0 of the entry. See complete history


Literature

Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron

Fukuyama, K.Okada, T.

(2007) Acta Crystallogr D Biol Crystallogr 63: 472-477

  • DOI: 10.1107/S0907444907003812
  • Primary Citation of Related Structures:  
    2E39, 2E3A, 2E3B

  • PubMed Abstract: 
  • 1.3 A resolution crystal structures of the cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosus peroxidase (ARP), a class II peroxidase belonging to the plant peroxidase superfamily, have been determined. Anisotropic temperature factors were introduced for all non-H atoms of these complexes using SHELX-97 and stereochemical constraints were applied to the protein, protoporphyrin and sugar moieties, but not to the coordination geometries to the haem iron ...

    1.3 A resolution crystal structures of the cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosus peroxidase (ARP), a class II peroxidase belonging to the plant peroxidase superfamily, have been determined. Anisotropic temperature factors were introduced for all non-H atoms of these complexes using SHELX-97 and stereochemical constraints were applied to the protein, protoporphyrin and sugar moieties, but not to the coordination geometries to the haem iron. These refinements identified multiple conformations for several side chains and revised the side-chain conformations of several residues. Little difference was observed in the structures of the polypeptides, haem and sugar moieties and in the coordinations to two calcium ions in these complexes. Characteristic coordination geometries of each ligand to the haem iron were observed. CN(-) binds to the haem iron in a tilt mode (Fe...C-N = 170 degrees ), whereas NO and hydroxylamine bind in bent modes (Fe...N-O = 125 degrees and Fe...NH(2)-OH = 111 degrees ). CN(-) is directed toward the distal histidine (His56) and forms a hydrogen bond with the N(epsilon) atom, whereas NO and hydroxylamine are directed away from His56. The Fe atoms of ARP-CN and ARP-NO, in which the haem irons are both in low-spin states, are approximately in the pyrrole N plane, whereas the iron in native ARP, which is in a five-coordinated high-spin state, deviates markedly from the plane.


    Related Citations: 
    • Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases
      Kunishima, N., Fukuyama, K., Matsubara, H., Hatanaka, H., Shibano, Y., Amachi, T.
      (1994) J Mol Biol 235: 331

    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan. fukuyama@bio.sci.osaka-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PeroxidaseA344Agaricales sp. 'Arthromyces ramosusMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for P28313 (Arthromyces ramosus)
Explore P28313 
Go to UniProtKB:  P28313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28313
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
F [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.84α = 90
b = 73.84β = 90
c = 115.68γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary