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- PDB-8qx0: Ligninolytic manganese peroxidase Ape-MnP1 from Agaricales mushro... -

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Basic information

Entry
Database: PDB / ID: 8qx0
TitleLigninolytic manganese peroxidase Ape-MnP1 from Agaricales mushrooms in complex with a manganese ion
ComponentsPeroxidase
KeywordsOXIDOREDUCTASE / Manganese peroxidase / Fungal / ligninolytic
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase ...Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / DI(HYDROXYETHYL)ETHER / Peroxidase
Similarity search - Component
Biological speciesAgrocybe pediades (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.247 Å
AuthorsSantillana, E. / Romero, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish National Research Council Spain
CitationJournal: Biotechnol Biofuels Bioprod / Year: 2024
Title: Structure-function characterization of two enzymes from novel subfamilies of manganese peroxidases secreted by the lignocellulose-degrading Agaricales fungi Agrocybe pediades and Cyathus striatus.
Authors: Sanchez-Ruiz, M.I. / Santillana, E. / Linde, D. / Romero, A. / Martinez, A.T. / Ruiz-Duenas, F.J.
History
DepositionOct 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0879
Polymers34,9251
Non-polymers1,1628
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-37 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.630, 39.811, 63.560
Angle α, β, γ (deg.)90.000, 101.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peroxidase / Manganese peroxidase


Mass: 34925.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe pediades (fungus) / Gene: D9613_004605 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4QK56, manganese peroxidase

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Non-polymers , 6 types, 187 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 30% P2000 MME, 0,1 M sodium citrate, pH 4.2

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.24→62.29 Å / Num. obs: 81601 / % possible obs: 95.2 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.068 / Net I/σ(I): 10
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3964 / CC1/2: 0.539 / Rpim(I) all: 0.493 / Rrim(I) all: 0.7 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.247→62.284 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.784 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1989 4019 4.926 %
Rwork0.1775 77575 -
all0.179 --
obs-81594 95.081 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.623 Å2
Baniso -1Baniso -2Baniso -3
1--0.048 Å20 Å20.415 Å2
2---0.581 Å2-0 Å2
3---0.424 Å2
Refinement stepCycle: LAST / Resolution: 1.247→62.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 73 179 2702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122587
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162429
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.8173538
X-RAY DIFFRACTIONr_angle_other_deg1.3621.7325629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.66958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85310382
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.8011097
X-RAY DIFFRACTIONr_chiral_restr0.1050.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023021
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02533
X-RAY DIFFRACTIONr_nbd_refined0.2290.2579
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22285
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21345
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0630.23
X-RAY DIFFRACTIONr_nbd_other0.1560.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0840.214
X-RAY DIFFRACTIONr_mcbond_it1.2711.181343
X-RAY DIFFRACTIONr_mcbond_other1.2691.1791343
X-RAY DIFFRACTIONr_mcangle_it1.8662.1211678
X-RAY DIFFRACTIONr_mcangle_other1.8692.1221679
X-RAY DIFFRACTIONr_scbond_it2.3771.4091244
X-RAY DIFFRACTIONr_scbond_other2.3791.4111245
X-RAY DIFFRACTIONr_scangle_it3.4212.4541856
X-RAY DIFFRACTIONr_scangle_other3.422.4551857
X-RAY DIFFRACTIONr_lrange_it3.9111.8062915
X-RAY DIFFRACTIONr_lrange_other3.88911.1462885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.247-1.2790.3032800.29356630.29462850.9320.93994.55850.28
1.279-1.3140.2852920.26555270.26661360.9480.94894.83380.246
1.314-1.3530.2412710.24453770.24459920.9590.95694.2590.22
1.353-1.3940.2342350.22251950.22358070.9580.96593.50780.196
1.394-1.440.2182740.20750920.20756260.9680.96995.37860.181
1.44-1.490.2122670.19349300.19454470.9670.97495.41030.167
1.49-1.5470.1862420.17647990.17752880.9760.97995.3290.152
1.547-1.610.1872250.1643660.16150520.9760.98390.87490.14
1.61-1.6810.1852220.15444320.15548770.9780.98495.42750.136
1.681-1.7630.1762560.14842100.1546410.9810.98696.22930.134
1.763-1.8580.1772020.14941240.1544500.9790.98697.21350.138
1.858-1.9710.1912070.15338160.15541830.9780.98596.1750.147
1.971-2.1070.1851790.15635010.15739610.9760.98592.90580.155
2.107-2.2760.181820.15634160.15736710.9780.98598.01140.159
2.276-2.4930.1591850.1531730.1534150.9850.98698.33090.159
2.493-2.7860.1851390.16927590.1730590.9820.98394.73680.183
2.786-3.2160.231270.1924200.19227370.9670.97793.05810.213
3.216-3.9360.222960.18722140.18823320.9710.97899.05660.22
3.936-5.5560.171790.17116010.17118040.9770.98493.12640.217
5.556-62.2840.217590.1929600.19310520.9780.97996.86310.254

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