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- PDB-9jlh: STRUCTURE OF MUTANT3 OF UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA -

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Basic information

Entry
Database: PDB / ID: 9jlh
TitleSTRUCTURE OF MUTANT3 OF UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA
ComponentsAromatic peroxygenase
KeywordsOXIDOREDUCTASE / PEROXYGENASE / CATALYSIS
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: 1.61 Å
AuthorsZhang, J. / Huang, Y.W. / Cheng, Y.Y. / Liu, W.D. / Zhang, W.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: STRUCTURE OF MUTANT3 OF UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA
Authors: Zhang, J. / Huang, Y.W. / Cheng, Y.Y. / Liu, W.D. / Zhang, W.Y.
History
DepositionSep 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 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)37,3106
Polymers36,0051
Non-polymers1,3045
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-13 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.301, 57.952, 60.910
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aromatic peroxygenase / AaP


Mass: 36005.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Q115K, G238A, G284V / Source: (gene. exp.) Cyclocybe aegerita (fungus) / Gene: APO1 / Production host: Komagataella pastoris (fungus) / References: UniProt: B9W4V6, unspecific peroxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG, NaCl,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.61→57.3 Å / Num. obs: 43650 / % possible obs: 99.3 % / Redundancy: 10.5 % / CC1/2: 0.977 / Net I/σ(I): 11.3
Reflection shellResolution: 1.61→1.69 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6099 / CC1/2: 0.691 / Χ2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→48.26 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 16.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 2016 4.65 %
Rwork0.1587 --
obs0.1598 43355 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 86 447 3056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112686
X-RAY DIFFRACTIONf_angle_d1.0683672
X-RAY DIFFRACTIONf_dihedral_angle_d9.52423
X-RAY DIFFRACTIONf_chiral_restr0.068390
X-RAY DIFFRACTIONf_plane_restr0.016491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.670.26482040.24553888X-RAY DIFFRACTION95
1.67-1.730.23691780.20974121X-RAY DIFFRACTION100
1.73-1.810.2312140.17624147X-RAY DIFFRACTION100
1.81-1.910.20311980.17864149X-RAY DIFFRACTION100
1.91-2.030.20172110.18144138X-RAY DIFFRACTION100
2.03-2.190.1852000.15324148X-RAY DIFFRACTION100
2.19-2.40.18081900.1544176X-RAY DIFFRACTION100
2.41-2.750.18352130.14354144X-RAY DIFFRACTION100
2.75-3.470.16651980.13964183X-RAY DIFFRACTION100
3.47-48.260.14562100.14084245X-RAY DIFFRACTION100

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