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- PDB-4blk: Crystal Structure of Fungal Versatile Peroxidase I from Pleurotus... -

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Basic information

Entry
Database: PDB / ID: 4blk
TitleCrystal Structure of Fungal Versatile Peroxidase I from Pleurotus ostreatus - Crystal Form I
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: 1.049 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 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _citation.page_last / _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.title / _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 2.1Nov 20, 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)35,4924
Polymers34,7951
Non-polymers6973
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.500, 96.500, 38.380
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.45 Å3/Da / Density % sol: 49.78 % / Description: NONE
Crystal growDetails: 0.1 M NA-ACETATE PH 4.6, 8% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / 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: 1.05→50 Å / Num. obs: 156095 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 9.11 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.3
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / % possible all: 66.9

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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: 1.049→43.156 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 11.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1369 7803 5 %
Rwork0.1304 --
obs0.1308 156081 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.049→43.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 45 452 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082560
X-RAY DIFFRACTIONf_angle_d1.2883504
X-RAY DIFFRACTIONf_dihedral_angle_d13.492911
X-RAY DIFFRACTIONf_chiral_restr0.07385
X-RAY DIFFRACTIONf_plane_restr0.007472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0491-1.0610.28481260.3312208X-RAY DIFFRACTION43
1.061-1.07350.3121410.30793061X-RAY DIFFRACTION58
1.0735-1.08660.291820.28723625X-RAY DIFFRACTION70
1.0866-1.10030.24442130.25224187X-RAY DIFFRACTION80
1.1003-1.11480.24742520.23234519X-RAY DIFFRACTION88
1.1148-1.13010.2022550.21164942X-RAY DIFFRACTION93
1.1301-1.14620.18652690.18715099X-RAY DIFFRACTION99
1.1462-1.16330.17582790.17135215X-RAY DIFFRACTION99
1.1633-1.18150.16632720.15845145X-RAY DIFFRACTION100
1.1815-1.20090.16012720.14635238X-RAY DIFFRACTION100
1.2009-1.22160.15392750.14055252X-RAY DIFFRACTION100
1.2216-1.24380.14412730.13595167X-RAY DIFFRACTION100
1.2438-1.26770.13582750.12865229X-RAY DIFFRACTION100
1.2677-1.29360.13092750.1235212X-RAY DIFFRACTION100
1.2936-1.32170.12992800.11945224X-RAY DIFFRACTION100
1.3217-1.35250.13852750.11425201X-RAY DIFFRACTION100
1.3525-1.38630.11942770.10885241X-RAY DIFFRACTION100
1.3863-1.42380.1142780.1045263X-RAY DIFFRACTION100
1.4238-1.46570.10892730.10165181X-RAY DIFFRACTION100
1.4657-1.5130.1022730.10215228X-RAY DIFFRACTION100
1.513-1.56710.09752750.0995242X-RAY DIFFRACTION100
1.5671-1.62980.11332770.10115236X-RAY DIFFRACTION100
1.6298-1.7040.11712750.10095233X-RAY DIFFRACTION100
1.704-1.79390.10352740.10735256X-RAY DIFFRACTION100
1.7939-1.90620.12432750.1125265X-RAY DIFFRACTION100
1.9062-2.05340.12842770.11345271X-RAY DIFFRACTION100
2.0534-2.26010.11272880.11055280X-RAY DIFFRACTION100
2.2601-2.58710.13422760.12025278X-RAY DIFFRACTION100
2.5871-3.25930.14732840.14075331X-RAY DIFFRACTION100
3.2593-43.19270.14212870.14165449X-RAY DIFFRACTION100

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