2E3B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.,SECT.D 63: 472-477

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

  • 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 f ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxidase
A
344Arthromyces ramosusEC: 1.11.1.7
Find proteins for P28313 (Arthromyces ramosus)
Go to UniProtKB:  P28313
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
HOA
Query on HOA

Download SDF File 
Download CCD File 
A
HYDROXYAMINE
H3 N O
AVXURJPOCDRRFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.141 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.150α = 90.00
b = 73.150β = 90.00
c = 114.940γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
SHELXL-97refinement
MAR345data collection
MOSFLMdata reduction
SHELXrefinement
X-PLORphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description