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- PDB-1arp: Crystal structure of the fungal peroxidase from Arthromyces ramos... -

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Basic information

Entry
Database: PDB / ID: 1arp
TitleCrystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 angstroms resolution: structural comparisons with the lignin and cytochrome C peroxidases
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 sourcePenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / 1.9 Å resolution
AuthorsKunishima, N. / Fukuyama, K.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases.
Authors: Kunishima, N. / Fukuyama, K. / Matsubara, H. / Hatanaka, H. / Shibano, Y. / Amachi, T.
#1: 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: Jun 18, 1993 / Release: Jan 31, 1994
RevisionDateData content typeGroupProviderType
1.0Jan 31, 1994Structure 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)36,8626
Polyers35,7231
Non-polymers1,1395
Water4,432246
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE MOLECULE.

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Components

#1: Protein/peptide PEROXIDASE /


Mass: 35722.797 Da / Num. of mol.: 1 / Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P28313, peroxidase
#2: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


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


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


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


Mass: 18.015 Da / Num. of mol.: 246 / Formula: H2O / Water
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PER_COPCI SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE - GLY 4 VAL 100 ILE 100 THERE ARE TWO VARIANTS VAL/ILE AT THIS POSITION AND VAL VARIANT PREDOMINATES. THE AUTHORS' SEQUENCING RESULTS FOR ARP ARE CONSISTENT WITH THOSE FROM COPRINUS PEROXIDASE REPORTED BY BAUNSGAARD ET AL. (1993) EXCEPT THAT ARP HAS AN INSERTION OF GLYCINE AT THE AMINO TERMINAL GLYCINE-RUCH REGION. THEY REPORTED THAT TWO VARIANTS ARE PRESENT IN COPRINUS CINEREUS PEROXIDASE (VAL/ILE AT 99TH POSITION) AND THAT THE VAL VARIANT PREDOMINATES. THE AUTHORS' X-RAY ANALYSIS SUGGESTS THAT THE CORRESPONDING POSITION IN ARP IS OCCUPIED BY ILE; THE ELECTRON DENSITY FOR CD ILE 100 IS CLEAR IN THE FINAL 2FO-FC MAP.

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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 grow
*PLUS
Temp: 24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: used as seeds, referred to 'Kunishima, N.', (1993) 'Proteins.Struct.,Funct., Genet.', 15, 216-220
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120-40 mg/mlARP1drop
232 %satammonium sulfate1reservoir
320 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 1.9 Å / Number obs: 19789 / Number measured all: 83158 / Rmerge I obs: 0.0582

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.174 / R factor obs: 0.174 / Highest resolution: 1.9 Å / Lowest resolution: 7 Å
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 2465 / Nucleic acid: 0 / Ligand: 73 / Solvent: 246 / Total: 2784
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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
Least-squares process
*PLUS
R factor obs: 0.174 / Highest resolution: 1.9 Å / Lowest resolution: 7 Å / Number reflection obs: 19191
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.058
X-RAY DIFFRACTIONx_plane_restr0.031
X-RAY DIFFRACTIONx_chiral_restr0.131

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