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- PDB-4bly: CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS... -

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Basic information

Entry
Database: PDB / ID: 4bly
TitleCRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM V
ComponentsVERSATILE PEROXIDASE I
KeywordsOXIDOREDUCTASE / CLASS II FUNGAL PEROXIDASES
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 VPL1
Similarity search - Component
Biological speciesPLEUROTUS OSTREATUS (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: Biotechnol.Biofuels / Year: 2014
Title: Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability.
Authors: Fernandez-Fueyo, E. / Ruiz-Duenas, F.J. / Martinez, M.J. / Romero, A. / Hammel, K.E. / Medrano, F.J. / Martinez, A.T.
History
DepositionMay 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VERSATILE PEROXIDASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5885
Polymers34,7951
Non-polymers7934
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.780, 93.780, 38.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein VERSATILE PEROXIDASE I


Mass: 34794.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLEUROTUS OSTREATUS (oyster mushroom) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): W3110 / References: UniProt: Q9UR19*PLUS, versatile peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.51 % / Description: NONE
Crystal growDetails: 0.1 M NA-HEPES AT PH 7.5, 1.6 M (NH4)2SO4 & 2 % PEG 1000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 31336 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 2
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 1.6 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FMU

3fmu


Resolution: 1.794→41.94 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 1555 5 %
Rwork0.1657 --
obs0.1675 31258 99.21 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.594 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9846 Å20 Å20 Å2
2--0.9846 Å20 Å2
3----1.9691 Å2
Refinement stepCycle: LAST / Resolution: 1.794→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 50 302 2778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162546
X-RAY DIFFRACTIONf_angle_d1.593488
X-RAY DIFFRACTIONf_dihedral_angle_d14.141899
X-RAY DIFFRACTIONf_chiral_restr0.113385
X-RAY DIFFRACTIONf_plane_restr0.009468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7944-1.85230.34031310.29042486X-RAY DIFFRACTION92
1.8523-1.91850.30471410.25352718X-RAY DIFFRACTION100
1.9185-1.99530.29831390.21442693X-RAY DIFFRACTION100
1.9953-2.08610.21781420.1832682X-RAY DIFFRACTION100
2.0861-2.19610.21921390.16622695X-RAY DIFFRACTION100
2.1961-2.33370.21721370.15712701X-RAY DIFFRACTION100
2.3337-2.51390.19611470.15742709X-RAY DIFFRACTION100
2.5139-2.76680.17521420.15462719X-RAY DIFFRACTION100
2.7668-3.16710.20011390.15582726X-RAY DIFFRACTION100
3.1671-3.98970.17361450.13732747X-RAY DIFFRACTION100
3.9897-41.95110.16691530.15452827X-RAY DIFFRACTION100

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