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- PDB-2e3a: Crystal structure of the NO-bound form of Arthromyces ramosus per... -

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Basic information

Entry
Database: PDB / ID: 2e3a
TitleCrystal structure of the NO-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution
ComponentsPeroxidase
KeywordsOXIDOREDUCTASE / heme protein / coordination geometry of heme iron / ARP / peroxidase
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 / alpha-D-mannopyranose / NITRIC OXIDE / Peroxidase
Similarity search - Component
Biological species'Arthromyces ramosus' (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsFukuyama, K. / Okada, T.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: 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
Authors: Fukuyama, K. / Okada, T.
#1: 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.
History
DepositionNov 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_conn_type / 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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_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.conn_type_id / _struct_conn.id / _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 / _struct_conn_type.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 / _database_2.pdbx_database_accession

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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)37,0547
Polymers35,7231
Non-polymers1,3316
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.770, 73.770, 115.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe biological assembly is a monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peroxidase


Mass: 35722.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 'Arthromyces ramosus' (fungus) / Genus: 'Arthromyces' / References: UniProt: P28313, peroxidase

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Sugars , 2 types, 2 molecules

#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: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 407 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 297 K / Method: microdialysis / pH: 7.5
Details: 37% saturated ammonium sulfate, Tris-HCl, pH 7.5, MICRODIALYSIS, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2001
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 78980 / Num. obs: 78980 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 3.2
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 0.8 / Num. measured all: 67847 / Num. unique all: 10689 / Rsym value: 0.264 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
SHELXL-97refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.3→10 Å / Num. parameters: 26674 / Num. restraintsaints: 32117 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 3892 5.3 %RANDOM
Rwork0.148 ---
all0.1528 73645 --
obs0.1528 73645 --
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1515 / Occupancy sum non hydrogen: 2952.14
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 86 403 2954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0294
X-RAY DIFFRACTIONs_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.07

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