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

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Basic information

Entry
Database: PDB / ID: 4blx
TitleCRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM IV
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: 1.249 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 1.2Nov 13, 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
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.670, 94.670, 38.460
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.: 430 / 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: 2.36 Å3/Da / Density % sol: 47.93 % / Description: NONE
Crystal growDetails: 20 % PEG 3350, 0.2 M AMMONIUM FORMATE.

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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: 1.25→50 Å / Num. obs: 94526 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 12.14 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.8
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.9 / % possible all: 95.7

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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: 1.249→47.335 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 4702 5 %
Rwork0.1597 --
obs0.1607 94369 99.31 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.233 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.667 Å20 Å20 Å2
2--0.667 Å20 Å2
3----1.3339 Å2
Refinement stepCycle: LAST / Resolution: 1.249→47.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 45 430 2905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122560
X-RAY DIFFRACTIONf_angle_d1.5363505
X-RAY DIFFRACTIONf_dihedral_angle_d14.513910
X-RAY DIFFRACTIONf_chiral_restr0.094386
X-RAY DIFFRACTIONf_plane_restr0.009472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2485-1.26270.43861330.41132501X-RAY DIFFRACTION82
1.2627-1.27760.35411500.29842963X-RAY DIFFRACTION99
1.2776-1.29310.29231580.28352941X-RAY DIFFRACTION100
1.2931-1.30950.30481560.25173016X-RAY DIFFRACTION100
1.3095-1.32670.28321550.25093006X-RAY DIFFRACTION100
1.3267-1.34490.25691580.22762935X-RAY DIFFRACTION100
1.3449-1.36410.22871590.2112965X-RAY DIFFRACTION100
1.3641-1.38450.23571590.20353011X-RAY DIFFRACTION100
1.3845-1.40610.24721540.19192957X-RAY DIFFRACTION100
1.4061-1.42920.20751590.16893014X-RAY DIFFRACTION100
1.4292-1.45380.19421560.16042981X-RAY DIFFRACTION100
1.4538-1.48030.17131590.15113020X-RAY DIFFRACTION100
1.4803-1.50870.17791510.14662948X-RAY DIFFRACTION100
1.5087-1.53950.17631610.14483013X-RAY DIFFRACTION100
1.5395-1.5730.16771570.13682995X-RAY DIFFRACTION100
1.573-1.60960.18291580.14123006X-RAY DIFFRACTION100
1.6096-1.64990.16521540.14112993X-RAY DIFFRACTION100
1.6499-1.69450.17761570.13443005X-RAY DIFFRACTION100
1.6945-1.74430.15521530.13543004X-RAY DIFFRACTION100
1.7443-1.80060.16461560.14042981X-RAY DIFFRACTION100
1.8006-1.8650.16541610.14343004X-RAY DIFFRACTION100
1.865-1.93970.19251630.15143038X-RAY DIFFRACTION100
1.9397-2.0280.16511570.15363006X-RAY DIFFRACTION100
2.028-2.13490.16891580.15073018X-RAY DIFFRACTION100
2.1349-2.26860.16661550.14883030X-RAY DIFFRACTION100
2.2686-2.44380.1631560.14353022X-RAY DIFFRACTION100
2.4438-2.68970.16531620.1543021X-RAY DIFFRACTION100
2.6897-3.07880.17061610.15563043X-RAY DIFFRACTION100
3.0788-3.87870.15051610.14983067X-RAY DIFFRACTION100
3.8787-47.3690.1741650.15963163X-RAY DIFFRACTION100

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