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- PDB-1arw: CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHRO... -

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Entry
Database: PDB / ID: 1arw
TitleCRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS
ComponentsPEROXIDASE
KeywordsPEROXIDASE (DONOR:H2O2 OXIDOREDUCTASE)
Function / homologyHaem peroxidase superfamily / Peroxidase, active site / Plant heme peroxidase family profile. / Peroxidases active site signature. / Peroxidases proximal heme-ligand signature. / Fungal peroxidase extension region / Peroxidase / Fungal ligninase / Haem peroxidase / Fungal ligninase, C-terminal ...Haem peroxidase superfamily / Peroxidase, active site / Plant heme peroxidase family profile. / Peroxidases active site signature. / Peroxidases proximal heme-ligand signature. / Fungal peroxidase extension region / Peroxidase / Fungal ligninase / Haem peroxidase / Fungal ligninase, C-terminal / Peroxidases heam-ligand binding site / peroxidase / peroxidase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding / Peroxidase
Function and homology information
Specimen source'Arthromyces ramosus' (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.6 Å resolution
AuthorsFukuyama, K. / Kunishima, N. / Amada, F.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.
Authors: Fukuyama, K. / Kunishima, N. / Amada, F. / Kubota, T. / Matsubara, H.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of the Fungal Peroxidase from Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases
Authors: Kunishima, N. / Fukuyama, K. / Matsubara, H. / Hatanaka, H. / Shibano, Y. / Amachi, T.
#2: Journal: Proteins / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase from a Fungus Arthromyces Ramosus
Authors: Kunishima, N. / Fukuyama, K. / Wakabayashi, S. / Sumida, M. / Takaya, M. / Shibano, Y. / Amachi, T. / Matsubara, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 25, 1995 / Release: Jan 29, 1996
RevisionDateData content typeGroupProviderType
1.0Jan 29, 1996Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8887
Polyers35,7231
Non-polymers1,1656
Water5,170287
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)74.570, 74.570, 117.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP 42 21 2

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide PEROXIDASE /


Mass: 35722.797 Da / Num. of mol.: 1 / Details: PH 4.0 / Source: (natural) 'Arthromyces ramosus' (fungus) / Genus: 'Arthromyces' / References: UniProt: P28313, peroxidase

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Non-polymers , 5 types, 293 molecules

#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Formula: CN / Cyanide
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Formula: C34H32FeN4O4 / Heme
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 / Density percent sol: 46.14 %
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
Temp: 24 ℃ / Method: vapor diffusion, hanging drop / Details: seeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120-40 MARP1drop
232 %satammonium sulfate1reservoir
320 mMTris-HCl1reservoir

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Data collection

SourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection
*PLUS
D resolution high: 1.6 Å / Number obs: 37412 / Number measured all: 158600 / Percent possible obs: 84.5 / Rmerge I obs: 0.0711

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.185 / R factor obs: 0.185 / Highest resolution: 1.6 Å / Lowest resolution: 7 Å
Refine hist #LASTHighest resolution: 1.6 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 2465 / Nucleic acid: 0 / Ligand: 75 / Solvent: 287 / Total: 2827
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine
*PLUS
Sigma F: 2
Displacement parameters
*PLUS
B iso mean: 16.8 Å2
Least-squares process
*PLUS
Number reflection obs: 36865
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.052
X-RAY DIFFRACTIONx_dihedral_angle_d3.2
X-RAY DIFFRACTIONx_plane_restr0.026
X-RAY DIFFRACTIONx_chiral_restr0.133

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