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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 / homology
Function and homology information


peroxidase / lactoperoxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site ...Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
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.
History
DepositionJun 18, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8445
Polymers35,7231
Non-polymers1,1214
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
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-MP42212
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE MOLECULE.

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Components

#1: Protein PEROXIDASE


Mass: 35722.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P28313, peroxidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 Å3/Da / Density % sol: 46.14 %
Crystal grow
*PLUS
Temperature: 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
IDConc.Common 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
Highest resolution: 1.9 Å / Num. obs: 19789 / Num. 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
RefinementResolution: 1.9→7 Å / Rfactor Rwork: 0.174 / Rfactor obs: 0.174
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 73 246 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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 7 Å / Num. reflection obs: 19191 / σ(F): 2 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
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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