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

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Basic information

Entry
Database: PDB / ID: 4bll
TitleCrystal Structure of Fungal Versatile Peroxidase I from Pleurotus ostreatus - Crystal Form II
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: 1.099 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 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
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 / struct_conn / struct_site
Item: _citation.country / _citation.page_last ..._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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 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)35,6887
Polymers34,7951
Non-polymers8936
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 62.900, 99.170
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.26 % / Description: NONE
Crystal growDetails: 0.1 M NA-ACETATE AT PH 4.5 & 20 % PEG-1000, 0.2 M ZN(OAC)2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1
DetectorDate: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 154452 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Biso Wilson estimate: 9.33 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3
Reflection shellResolution: 1.1→1.17 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.6 / % possible all: 93.5

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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: 1.099→44.477 Å / SU ML: 0.08 / σ(F): 1.42 / Phase error: 11.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1356 7481 5 %
Rwork0.1232 --
obs0.1238 150017 96.21 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.099→44.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 48 401 2802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112473
X-RAY DIFFRACTIONf_angle_d1.4833381
X-RAY DIFFRACTIONf_dihedral_angle_d13.495874
X-RAY DIFFRACTIONf_chiral_restr0.088373
X-RAY DIFFRACTIONf_plane_restr0.009453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0992-1.11170.28111600.26953224X-RAY DIFFRACTION66
1.1117-1.12480.26482050.24183971X-RAY DIFFRACTION80
1.1248-1.13850.22192270.21814228X-RAY DIFFRACTION87
1.1385-1.15290.22712300.19754443X-RAY DIFFRACTION90
1.1529-1.16810.18322400.18234613X-RAY DIFFRACTION93
1.1681-1.18410.15922430.16444684X-RAY DIFFRACTION95
1.1841-1.2010.17252540.15624719X-RAY DIFFRACTION96
1.201-1.21890.16892520.15174776X-RAY DIFFRACTION97
1.2189-1.2380.17642550.14724808X-RAY DIFFRACTION97
1.238-1.25830.15512490.1364807X-RAY DIFFRACTION97
1.2583-1.280.13692540.12744827X-RAY DIFFRACTION98
1.28-1.30320.13462530.1234833X-RAY DIFFRACTION98
1.3032-1.32830.13062580.11664858X-RAY DIFFRACTION99
1.3283-1.35540.13582440.11284843X-RAY DIFFRACTION98
1.3554-1.38490.12372530.10644847X-RAY DIFFRACTION99
1.3849-1.41710.13052660.10334940X-RAY DIFFRACTION99
1.4171-1.45260.11972540.09764877X-RAY DIFFRACTION99
1.4526-1.49180.11382650.0944921X-RAY DIFFRACTION99
1.4918-1.53570.1042570.09144903X-RAY DIFFRACTION99
1.5357-1.58530.1022600.08934916X-RAY DIFFRACTION100
1.5853-1.6420.11642550.09334902X-RAY DIFFRACTION100
1.642-1.70770.11172600.09124944X-RAY DIFFRACTION100
1.7077-1.78540.10432640.09964890X-RAY DIFFRACTION100
1.7854-1.87960.12532620.10294931X-RAY DIFFRACTION100
1.8796-1.99730.12442560.10794951X-RAY DIFFRACTION100
1.9973-2.15160.10242590.10684970X-RAY DIFFRACTION100
2.1516-2.36810.11862620.11014950X-RAY DIFFRACTION100
2.3681-2.71070.13332610.12074959X-RAY DIFFRACTION100
2.7107-3.4150.15042590.13984979X-RAY DIFFRACTION100
3.415-44.51340.14822640.1385022X-RAY DIFFRACTION100

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