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- PDB-5ag1: DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with ... -

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Basic information

Entry
Database: PDB / ID: 5ag1
TitleDyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with meso- nitrated heme
ComponentsDYE-DECOLORIZING PEROXIDASE
KeywordsOXIDOREDUCTASE / DYP / FUNGAL / HEME / GLYCOPROTEIN / NITRATION
Function / homology
Function and homology information


dye decolorizing peroxidase / peroxidase / lactoperoxidase activity / peroxidase activity / heme binding / extracellular region / metal ion binding / cytosol
Similarity search - Function
: / DyP dimeric alpha+beta barrel domain / : / Dyp-type peroxidase, C-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
CACODYLATE ION / FORMIC ACID / DELTA-MESO NITROHEME / NITRITE ION / Dye-decolorizing peroxidase AauDyP1
Similarity search - Component
Biological speciesAURICULARIA AURICULA-JUDAE (jelly ear fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStrittmatter, E. / Piontek, K. / Plattner, D.A.
CitationJournal: To be Published
Title: Crystallographic Trapping of a Covalently Modified Heme in a Dye-Decolorizing Peroxidase
Authors: Strittmatter, E. / Piontek, K. / Plattner, D.A.
History
DepositionJan 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: DYE-DECOLORIZING PEROXIDASE
B: DYE-DECOLORIZING PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,38922
Polymers93,6122
Non-polymers3,77720
Water16,087893
1
A: DYE-DECOLORIZING PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,93012
Polymers46,8061
Non-polymers2,12411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DYE-DECOLORIZING PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,45910
Polymers46,8061
Non-polymers1,6539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.000, 46.780, 148.150
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DYE-DECOLORIZING PEROXIDASE


Mass: 46805.855 Da / Num. of mol.: 2 / Fragment: DYP-TYPE PEROXIDASE DOMAIN, RESIDUES 64-509 / Source method: isolated from a natural source
Details: GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS NUMBER DSM 11326
Source: (natural) AURICULARIA AURICULA-JUDAE (jelly ear fungus)
Strain: SXM9-C021 / References: UniProt: I2DBY1, dye decolorizing peroxidase

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Sugars , 2 types, 5 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
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 908 molecules

#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-N7H / DELTA-MESO NITROHEME


Mass: 659.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H29FeN5O6
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsDELTA-MESO NITROHEME (N7H): IRON PROTOPORPHYRIN IX WITH A NITRO GROUP AT THE DELTA-MESO CARBON.
Sequence detailsPRECURSOR SEQUENCE IN GENBANK WITH PROLONGED N-TERMINUS.

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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: 44 % / Description: NONE
Crystal growpH: 6.5
Details: 0.17 M SODIUM ACETATE TRIHYDRATE, 0.085 M SODIUM CACODYLATE PH 6.5, 25% (W/V) PEG 8000, 15% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.85→44.57 Å / Num. obs: 75411 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.11
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AU9

4au9


Resolution: 1.85→44.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.131 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY PROTEIN WAS TREATED WITH PROLI NONOATE AND PERACETIC ACID PRIOR TO CRYSTALLIZATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.21547 3770 5 %RANDOM
Rwork0.17451 ---
obs0.17655 71625 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.65 Å2
2--0.17 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 243 893 7740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0197097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6741.9859708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93625292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71915994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7951528
X-RAY DIFFRACTIONr_chiral_restr0.0510.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215521
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8621.9183616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3433.2314534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2122.0483481
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 242 -
Rwork0.291 4603 -
obs--86.49 %

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