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- PDB-7oo5: Crystal structure of the lignin peroxidase (ApeLiP) from Agrocybe... -

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Basic information

Entry
Database: PDB / ID: 7oo5
TitleCrystal structure of the lignin peroxidase (ApeLiP) from Agrocybe pediades
Componentslignin peroxidase
KeywordsOXIDOREDUCTASE / ligninolytic peroxidase / plant cell-wall degrading enzyme
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesAgrocybe pediades (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRomero, A. / Ruiz-Duenas, F.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-77835-R Spain
Citation
Journal: Antioxidants / Year: 2021
Title: Agaricales Mushroom Lignin Peroxidase: From Structure-Function to Degradative Capabilities.
Authors: Sanchez-Ruiz, M.I. / Ayuso-Fernandez, I. / Rencoret, J. / Gonzalez-Ramirez, A.M. / Linde, D. / Davo-Siguero, I. / Romero, A. / Gutierrez, A. / Martinez, A.T. / Ruiz-Duenas, F.J.
#1: Journal: Mol.Biol.Evol. / Year: 2021
Title: Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity.
Authors: Ruiz-Duenas, F.J. / Barrasa, J.M. / Sanchez-Garcia, M. / Camarero, S. / Miyauchi, S. / Serrano, A. / Linde, D. / Babiker, R. / Drula, E. / Ayuso-Fernandez, I. / Pacheco, R. / Padilla, G. / ...Authors: Ruiz-Duenas, F.J. / Barrasa, J.M. / Sanchez-Garcia, M. / Camarero, S. / Miyauchi, S. / Serrano, A. / Linde, D. / Babiker, R. / Drula, E. / Ayuso-Fernandez, I. / Pacheco, R. / Padilla, G. / Ferreira, P. / Barriuso, J. / Kellner, H. / Castanera, R. / Alfaro, M. / Ramirez, L. / Pisabarro, A.G. / Riley, R. / Kuo, A. / Andreopoulos, W. / LaButti, K. / Pangilinan, J. / Tritt, A. / Lipzen, A. / He, G. / Yan, M. / Ng, V. / Grigoriev, I.V. / Cullen, D. / Martin, F. / Rosso, M.N. / Henrissat, B. / Hibbett, D. / Martinez, A.T.
History
DepositionMay 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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: lignin peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1286
Polymers34,3001
Non-polymers8275
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NULL
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-59 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.126, 74.950, 82.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein lignin peroxidase


Mass: 34300.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe pediades (fungus) / Production host: Escherichia coli (E. coli) / References: lignin peroxidase
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG500 MME, 100mM MES pH 6.5, 10mM ZnSO4

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.85→74.95 Å / Num. obs: 26316 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 36.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.026 / Rrim(I) all: 0.064 / Net I/σ(I): 15.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3 / Num. unique obs: 3760 / CC1/2: 0.931 / Rpim(I) all: 0.225 / Rrim(I) all: 0.569 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.14-3260refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLN

4bln


Resolution: 1.85→55.56 Å / SU ML: 0.2425 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.7508 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2687 1270 4.84 %
Rwork0.2318 24986 -
obs0.2336 26256 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.69 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 47 83 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082530
X-RAY DIFFRACTIONf_angle_d1.1383485
X-RAY DIFFRACTIONf_chiral_restr0.0562395
X-RAY DIFFRACTIONf_plane_restr0.0065460
X-RAY DIFFRACTIONf_dihedral_angle_d7.12471477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.41561400.35872733X-RAY DIFFRACTION99.83
1.92-2.010.33291300.31992719X-RAY DIFFRACTION99.82
2.01-2.120.34231290.2872763X-RAY DIFFRACTION99.66
2.12-2.250.36091520.27812717X-RAY DIFFRACTION99.9
2.25-2.420.36221320.26632780X-RAY DIFFRACTION99.86
2.42-2.660.34541340.26812767X-RAY DIFFRACTION99.83
2.66-3.050.30691540.26592763X-RAY DIFFRACTION99.76
3.05-3.840.28411540.23532798X-RAY DIFFRACTION99.46

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