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- PDB-9j1x: Structure of mutant evolved from PaDa-I, unspecific peroxygenase ... -

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Basic information

Entry
Database: PDB / ID: 9j1x
TitleStructure of mutant evolved from PaDa-I, unspecific peroxygenase from Agrocybe aegerita
ComponentsAromatic peroxygenase
KeywordsMETAL BINDING PROTEIN / mutant evolved from PaDa-I
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: 1.39 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 mutant evolved from PaDa-I, unspecific peroxygenase from Agrocybe aegerita
Authors: Liu, W. / Zhang, J. / Zhang, W.
History
DepositionAug 6, 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)36,9496
Polymers35,6451
Non-polymers1,3045
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-13 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.091, 57.907, 60.699
Angle α, β, γ (deg.)90.00, 110.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aromatic peroxygenase / AaP


Mass: 35644.723 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: obtained synthetically / 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: isolated from a natural source / 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.: 311 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate tetrahydrate (pH 7.2) and 20% w/v PEG 3350

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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, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.39→57.91 Å / Num. obs: 66880 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.251 / Net I/σ(I): 7.1
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 8.3 % / Rmerge(I) obs: 3.203 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4931 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→47.9 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.42 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 3336 4.99 %
Rwork0.1801 --
obs0.181 66806 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 86 311 2911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.098
X-RAY DIFFRACTIONf_dihedral_angle_d9.844423
X-RAY DIFFRACTIONf_chiral_restr0.083392
X-RAY DIFFRACTIONf_plane_restr0.012492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.440.28243360.25986316X-RAY DIFFRACTION100
1.44-1.50.25683410.23216294X-RAY DIFFRACTION100
1.5-1.570.23043160.2086349X-RAY DIFFRACTION100
1.57-1.650.22093440.20016305X-RAY DIFFRACTION100
1.65-1.750.20473230.19156322X-RAY DIFFRACTION100
1.75-1.890.19823360.18416347X-RAY DIFFRACTION100
1.89-2.080.20353230.18486341X-RAY DIFFRACTION100
2.08-2.380.17793460.1686332X-RAY DIFFRACTION100
2.38-2.990.18023290.17016401X-RAY DIFFRACTION100
2.99-47.90.17713420.15426463X-RAY DIFFRACTION100

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