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- PDB-3fm6: Crystal Structure Analysis of Fungal Versatile Peroxidase from Pl... -

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Basic information

Entry
Database: PDB / ID: 3fm6
TitleCrystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii
ComponentsVersatile peroxidase VPL2
KeywordsOXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / protoporphyrin IX / ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MN-INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS / MNII OXIDATION / PEROXIDASE / POLYVALENT PEROXIDASE / Heme / Hydrogen peroxide / Iron / Manganese / Metal-binding / Secreted / Zymogen
Function / homology
Function and homology information


versatile peroxidase / reactive-black-5:hydrogen-peroxide oxidoreductase activity / manganese peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / 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 / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site ...Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Versatile peroxidase VPL2
Similarity search - Component
Biological speciesPleurotus eryngii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsPiontek, K. / Martinez, A.T. / Choinowski, T. / Plattner, D.A.
CitationJournal: To be Published
Title: Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates
Authors: Piontek, K. / Choinowski, T. / Perez-Boada, M. / Ruiz-Duenas, F.J. / Martinez, M.J. / Plattner, D.A. / Martinez, A.T.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Versatile peroxidase VPL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,07416
Polymers34,5871
Non-polymers1,48715
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.333, 63.333, 99.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Versatile peroxidase VPL2 / Versatile liquid phase peroxidase 2


Mass: 34586.656 Da / Num. of mol.: 1 / Mutation: F142Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pleurotus eryngii (fungus) / Strain: IJFM, A169 / Gene: vpl2 / Plasmid: PFLAG1-VPL2 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 / References: UniProt: O94753, versatile peroxidase

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Non-polymers , 6 types, 549 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 16% PEG 8000, 100mM Zn-acetate, 100mM Na-cacodylate pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97992 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97992 Å / Relative weight: 1
ReflectionResolution: 1.13→40 Å / Num. all: 145501 / Num. obs: 145501 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.096 / Net I/σ(I): 13.5
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 7 / Num. unique all: 145501 / Rsym value: 0.156 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKG

3fkg


Resolution: 1.13→28.323 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.322 / SU ML: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11482 7291 5 %RANDOM
Rwork0.09965 ---
all0.1004 138344 --
obs0.1004 138206 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.13→28.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 67 534 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222568
X-RAY DIFFRACTIONr_bond_other_d0.0010.022313
X-RAY DIFFRACTIONr_angle_refined_deg1.4092.0213508
X-RAY DIFFRACTIONr_angle_other_deg0.7835358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06725.463108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19915375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5011510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
X-RAY DIFFRACTIONr_nbd_refined0.2290.3581
X-RAY DIFFRACTIONr_nbd_other0.2450.32477
X-RAY DIFFRACTIONr_nbtor_refined0.1830.51311
X-RAY DIFFRACTIONr_nbtor_other0.0930.51315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5618
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.586
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0720.22
X-RAY DIFFRACTIONr_mcbond_it1.96321649
X-RAY DIFFRACTIONr_mcbond_other1.6472652
X-RAY DIFFRACTIONr_mcangle_it2.69532631
X-RAY DIFFRACTIONr_scbond_it2.7952986
X-RAY DIFFRACTIONr_scangle_it3.7913864
X-RAY DIFFRACTIONr_rigid_bond_restr1.82432635
X-RAY DIFFRACTIONr_sphericity_free10.293542
X-RAY DIFFRACTIONr_sphericity_bonded4.8832482
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.141 533 -
Rwork0.118 10058 -
obs--98.82 %

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