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- PDB-3fm1: Crystal Structure Analysis of Fungal Versatile Peroxidase from Pl... -

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Basic information

Entry
Database: PDB / ID: 3fm1
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 / Calcium / Heme / Hydrogen peroxide / Iron / Manganese / Metal-binding / Organic radical / 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 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. ...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 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / 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: 1.78 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: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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: Versatile peroxidase VPL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,90716
Polymers34,6771
Non-polymers1,23015
Water13,547752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.645, 63.645, 99.598
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: 34676.777 Da / Num. of mol.: 1
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 , 7 types, 767 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHERE IS A CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THIS CAN BE ...THERE IS A CONFLICT BETWEEN THE REPORTED SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THIS CAN BE CALLED AS SPONTANEITY MUTATION. THE DEPOSITOR PREPARED THE TARGET PROTEIN AS WILD TYPE, BUT IN THE STRUCTURE ONE (SILENT) MUTATION WAS FOUND.

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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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9.0mg/ml protein in 10mM Na-tartrate pH 5.5, 17% PEG 10000, 200mM Zn-acetate, 100mM Na-cacodylate pH 6.5; Crystals were soaked with Mn2+; VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.74→25 Å / Num. all: 40092 / Num. obs: 40092 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 9.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 13.2
Reflection shellResolution: 1.74→1.78 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 2671 / Rsym value: 0.297 / % possible all: 99.4

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Processing

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

3fkg


Resolution: 1.78→24.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.187 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17241 1894 5.1 %RANDOM
Rwork0.1243 ---
obs0.12675 35577 98.66 %-
all-36060 --
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: 19.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.78→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 57 752 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222574
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0113523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27325.652115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83115375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8251510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.022031
X-RAY DIFFRACTIONr_nbd_refined0.2130.31393
X-RAY DIFFRACTIONr_nbtor_refined0.3180.51808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5861
X-RAY DIFFRACTIONr_metal_ion_refined0.3040.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.596
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_mcbond_it2.20521637
X-RAY DIFFRACTIONr_mcangle_it3.07632643
X-RAY DIFFRACTIONr_scbond_it2.9262958
X-RAY DIFFRACTIONr_scangle_it4.1663867
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 133 -
Rwork0.148 2699 -
obs--99.93 %

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