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- PDB-7d8m: Crystal structure of DyP -

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Basic information

Entry
Database: PDB / ID: 7d8m
TitleCrystal structure of DyP
ComponentsDye-decolorizing peroxidase
KeywordsOXIDOREDUCTASE / dye-decolorizing peroxidase
Function / homologyDyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / peroxidase activity / heme binding / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Dye-decolorizing peroxidase
Function and homology information
Biological speciesIrpex lacteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHe, C. / Jia, R. / Wang, T. / Li, L.Q.
CitationJournal: Biotechnol Biofuels / Year: 2021
Title: Revealing two important tryptophan residues with completely different roles in a dye-decolorizing peroxidase from Irpex lacteus F17.
Authors: Li, L. / Wang, T. / Chen, T. / Huang, W. / Zhang, Y. / Jia, R. / He, C.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dye-decolorizing peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6913
Polymers50,0431
Non-polymers6482
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-19 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.959, 118.959, 65.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Dye-decolorizing peroxidase


Mass: 50042.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Irpex lacteus (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P1C6N4
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate, 0.1M Sodium acetate trihydrate, 30% w/v PEG 4000, pH 4.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 35763 / % possible obs: 99.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.041 / Rrim(I) all: 0.132 / Χ2: 0.466 / Net I/σ(I): 2.9 / Num. measured all: 360800
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.037.90.81517760.9270.3060.8720.41199.7
2.03-2.078.30.81117560.9290.2950.8640.49599.9
2.07-2.119.80.7917880.9540.2650.8340.441100
2.11-2.1510.40.74417800.9540.2410.7830.447100
2.15-2.210.50.64517880.9570.2070.6780.44299.9
2.2-2.2510.50.59417700.9580.1920.6250.491100
2.25-2.3110.50.53917710.9610.1740.5670.47399.9
2.31-2.3710.20.42517860.9740.1390.4480.453100
2.37-2.44100.35317900.9790.1170.3730.453100
2.44-2.529.30.3118000.9830.1070.3280.49799.9
2.52-2.6110.80.27517850.9820.0880.2890.455100
2.61-2.7110.70.23617890.9880.0760.2480.46799.9
2.71-2.8410.60.18617830.9930.060.1960.471100
2.84-2.9910.50.14417660.9950.0470.1510.47399.9
2.99-3.1710.10.11117900.9960.0370.1170.47699.8
3.17-3.42100.08718010.9970.0290.0910.48399.9
3.42-3.7610.80.06717930.9970.0220.0710.46399.9
3.76-4.3110.60.05718020.9970.0190.060.46999.8
4.31-5.429.90.04818130.9980.0160.0510.39899.5
5.42-4010.20.06918360.9960.0220.0720.55298.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3afv

3afv


Resolution: 2→30.399 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1812 5.08 %
Rwork0.1689 33846 -
obs0.1709 35658 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.43 Å2 / Biso mean: 32.5222 Å2 / Biso min: 18.35 Å2
Refinement stepCycle: final / Resolution: 2→30.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 45 312 3844
Biso mean--25.13 36.48 -
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.05410.28611300.2424260099
2.0541-2.11450.27321340.22162571100
2.1145-2.18270.29361370.20172612100
2.1827-2.26070.23131550.19572588100
2.2607-2.35120.22941480.18612558100
2.3512-2.45820.23561190.17912596100
2.4582-2.58770.25991390.18932611100
2.5877-2.74970.2551300.18982613100
2.7497-2.96190.22251620.18282590100
2.9619-3.25960.21271580.17632580100
3.2596-3.73060.21571320.1632628100
3.7306-4.69740.17091360.13332633100
4.6974-30.3990.14181320.1418266699

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