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- PDB-9j1q: Structure of a mutant (PaDa-I) unspecific peroxygenase from Agroc... -

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Basic information

Entry
Database: PDB / ID: 9j1q
TitleStructure of a mutant (PaDa-I) unspecific peroxygenase from Agrocybe aegerita
ComponentsAromatic peroxygenase
KeywordsMETAL BINDING PROTEIN / unspecific peroxygenase
Function / homology
Function and homology information


unspecific peroxygenase / hydrogen peroxide catabolic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Chloroperoxidase / Chloroperoxidase-like superfamily / Peroxidase, family 2 / Heme haloperoxidase family profile.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Aromatic peroxygenase
Similarity search - Component
Biological speciesCyclocybe aegerita (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsLiu, W. / Zhang, J. / Zhang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of a mutant (PaDa-I) unspecific peroxygenase from Agrocybe aegerita
Authors: Liu, W. / Zhang, J. / Zhang, W.
History
DepositionAug 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aromatic peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6976
Polymers35,3921
Non-polymers1,3045
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-12 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 57.730, 58.770
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aromatic peroxygenase / AaP


Mass: 35392.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclocybe aegerita (fungus) / Gene: APO1 / Production host: Komagataella pastoris (fungus) / References: UniProt: B9W4V6, unspecific peroxygenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate (pH 6.0) and 20% w/v PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.34→57.73 Å / Num. obs: 69863 / % possible obs: 95.1 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.038 / Rrim(I) all: 0.123 / Χ2: 0.98 / Net I/σ(I): 13.7 / Num. measured all: 713427
Reflection shellResolution: 1.34→1.37 Å / % possible obs: 63 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.175 / Num. measured all: 23078 / Num. unique obs: 3447 / CC1/2: 0.603 / Rpim(I) all: 0.476 / Rrim(I) all: 1.274 / Χ2: 0.91 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→56.51 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.62 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1734 3491 5 %
Rwork0.1549 --
obs0.1558 69809 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→56.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 86 391 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.358
X-RAY DIFFRACTIONf_dihedral_angle_d10.238424
X-RAY DIFFRACTIONf_chiral_restr0.102387
X-RAY DIFFRACTIONf_plane_restr0.015493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.390.30222370.27544504X-RAY DIFFRACTION65
1.39-1.440.25353190.23036061X-RAY DIFFRACTION87
1.44-1.510.22773640.19156912X-RAY DIFFRACTION100
1.51-1.590.1943650.16436932X-RAY DIFFRACTION100
1.59-1.690.18543650.15456935X-RAY DIFFRACTION100
1.69-1.820.19563650.15486953X-RAY DIFFRACTION100
1.82-20.16653670.14566951X-RAY DIFFRACTION100
2-2.290.17343680.14146987X-RAY DIFFRACTION100
2.29-2.890.16053670.14676982X-RAY DIFFRACTION100
2.89-56.510.14363740.14277101X-RAY DIFFRACTION100

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