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- PDB-8qwt: Ligninolytic manganese peroxidase Cst-MnP1 from Agaricales mushro... -

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Basic information

Entry
Database: PDB / ID: 8qwt
TitleLigninolytic manganese peroxidase Cst-MnP1 from Agaricales mushrooms in complex with a manganese ion
ComponentsPeroxidase
KeywordsOXIDOREDUCTASE / Manganese peroxidase / Fungal / ligninolytic
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesCyathus striatus (fluted bird's nest fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.1Oct 23, 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

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Assembly

Deposited unit
A: Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,10613
Polymers34,4131
Non-polymers1,69312
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.790, 56.640, 109.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peroxidase / Manganese peroxidase


Mass: 34412.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyathus striatus (fluted bird's nest fungus)
Production host: Escherichia coli (E. coli) / References: manganese peroxidase

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Non-polymers , 7 types, 182 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 8000, 0,1 M Tris-HCl, pH 7, 0,3M MgCl2

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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: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→56.64 Å / Num. obs: 48414 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.076 / Rrim(I) all: 0.138 / Net I/σ(I): 8.3
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2237 / CC1/2: 0.638 / Rpim(I) all: 0.773 / Rrim(I) all: 1.389 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→54.755 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.159 / SU B: 1.666 / SU ML: 0.058 / Average fsc free: 0.9627 / Average fsc work: 0.9693 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1888 2432 5.031 %
Rwork0.1632 45904 -
all0.164 --
obs-48336 99.855 %
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: 16.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.362 Å20 Å2-0 Å2
2---1.688 Å20 Å2
3----0.674 Å2
Refinement stepCycle: LAST / Resolution: 1.5→54.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 104 170 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122581
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162377
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.8243527
X-RAY DIFFRACTIONr_angle_other_deg0.6711.7655492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.737510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10710343
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.69610103
X-RAY DIFFRACTIONr_chiral_restr0.0930.2394
X-RAY DIFFRACTIONr_chiral_restr_other0.040.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023047
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02563
X-RAY DIFFRACTIONr_nbd_refined0.240.2602
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22191
X-RAY DIFFRACTIONr_nbtor_refined0.180.21329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2139
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.222
X-RAY DIFFRACTIONr_nbd_other0.280.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.26
X-RAY DIFFRACTIONr_mcbond_it1.6291.6411327
X-RAY DIFFRACTIONr_mcbond_other1.6281.6411327
X-RAY DIFFRACTIONr_mcangle_it2.3872.9461658
X-RAY DIFFRACTIONr_mcangle_other2.3882.9481659
X-RAY DIFFRACTIONr_scbond_it2.3441.881254
X-RAY DIFFRACTIONr_scbond_other2.3411.881254
X-RAY DIFFRACTIONr_scangle_it3.4223.3081867
X-RAY DIFFRACTIONr_scangle_other3.4223.3091868
X-RAY DIFFRACTIONr_lrange_it4.42918.6762925
X-RAY DIFFRACTIONr_lrange_other4.42918.6812926
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
1.5-1.5390.2941880.28433410.28535380.9220.91599.74560.269
1.539-1.5810.3021790.26632240.26834090.9240.9399.8240.25
1.581-1.6270.2591690.2431570.24133310.9420.94599.84990.222
1.627-1.6770.251760.21130850.21332630.9490.95999.93870.194
1.677-1.7320.231330.19730410.19931780.9610.96799.87410.179
1.732-1.7930.221450.18429080.18630560.9580.97199.90180.166
1.793-1.860.2261440.16727830.16929300.9660.97799.89760.151
1.86-1.9360.1961430.15427040.15628510.9750.98399.85970.142
1.936-2.0220.1791470.14825980.1527480.9780.98599.89080.138
2.022-2.1210.1721180.14424860.14626070.980.98599.88490.137
2.121-2.2350.1851320.14423640.14625000.9740.98699.840.139
2.235-2.370.1751290.1422540.14223860.9810.98799.87430.139
2.37-2.5340.1711030.13821180.1422280.9780.98799.68580.137
2.534-2.7360.172970.1419870.14120870.9810.98799.85630.14
2.736-2.9970.214860.15518460.15819360.9680.98599.79340.16
2.997-3.3490.184830.15716610.15817470.9770.98599.82830.165
3.349-3.8650.139800.14814830.14715630.9890.9871000.159
3.865-4.7280.139830.13712680.13713510.9870.9891000.153
4.728-6.6610.177650.1739830.17310520.9820.98699.61980.189
6.661-54.7550.211320.176130.1726450.9790.9791000.182

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