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- PDB-4bm0: CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS... -

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Basic information

Entry
Database: PDB / ID: 4bm0
TitleCRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VII
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: 2.199 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 3, 2014Group: Data collection
Revision 1.2Dec 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 1.3Oct 23, 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
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.700, 96.700, 38.400
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.: 131 / 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: 2.46 Å3/Da / Density % sol: 50.02 % / Description: NONE
Crystal growDetails: 0.1 M NA-HEPES AT PH 7.5, 0.2 M NA-ACETATE & 20 % PEG 3000.

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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: 2.2→50 Å / Num. obs: 18474 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 26.83 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.1 / % possible all: 96.2

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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: 2.199→48.35 Å / SU ML: 0.28 / σ(F): 1.33 / Phase error: 32.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 904 5 %
Rwork0.2279 --
obs0.2301 18244 98.89 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.329 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2298 Å20 Å20 Å2
2--9.2298 Å20 Å2
3----18.4596 Å2
Refinement stepCycle: LAST / Resolution: 2.199→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 45 131 2602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052546
X-RAY DIFFRACTIONf_angle_d0.9233488
X-RAY DIFFRACTIONf_dihedral_angle_d14.657901
X-RAY DIFFRACTIONf_chiral_restr0.057386
X-RAY DIFFRACTIONf_plane_restr0.005469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1992-2.33690.37291470.32162742X-RAY DIFFRACTION95
2.3369-2.51740.38691490.31122886X-RAY DIFFRACTION100
2.5174-2.77070.33671540.28592880X-RAY DIFFRACTION100
2.7707-3.17150.29981480.25682899X-RAY DIFFRACTION99
3.1715-3.99550.26611540.20332911X-RAY DIFFRACTION100
3.9955-48.36170.17681520.17053022X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08880.0181-0.06450.1902-0.01690.04650.05760.1304-0.1211-0.3624-0.0613-0.1084-0.03670.1713-0.00070.38860.10990.08870.31560.00590.3014-22.8882-28.7735-2.241
20.3288-0.0643-0.03680.456-0.36020.41090.07060.0271-0.0504-0.35210.00630.04490.14810.15010.01110.34990.0234-0.00130.1306-0.02330.2079-38.3162-28.3871-2.8059
30.3937-0.1772-0.13650.2123-0.00320.0681-0.0021-0.04340.0515-0.14190.0589-0.0101-0.13670.08090.03660.3788-0.02170.0090.0591-0.01210.1677-37.3784-11.4667-1.7902
40.0504-0.02410.04070.20850.17870.282-0.05860.11030.0537-0.03820.02320.0136-0.24480.2511-0.00020.4258-0.06470.0420.283-0.01210.3128-30.1268-2.0789-1.2678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:50)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 51:159)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 160:279)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 280:330)

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