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- PDB-5abo: CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PL... -

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Basic information

Entry
Database: PDB / ID: 5abo
TitleCRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPi-br. MUTATED RESIDUES T2K, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, A309K AND A314R.
ComponentsVERSATILE PEROXIDASE VPL2
KeywordsOXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / PROTOPORPHYRIN IX / ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MN-INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS / MNII OXIDATION / PEROXIDASE / POLYVALENT PEROXIDASE / HEME / HYDROGEN PEROXIDE / IRON / MANGANESE / METAL-BINDING / SECRETED / ZYMOGEN
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 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site ...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 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Versatile peroxidase VPL2
Similarity search - Component
Biological speciesPLEUROTUS ERYNGII (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.095 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: Plos One / Year: 2015
Title: Improving the Ph-Stability of Versatile Peroxidase by Comparative Structural Analysis with a Naturally-Stable Manganese Peroxidase.
Authors: Saez-Jimenez, V. / Fernendez-Fueyo, E. / Medrano, F.J. / Romero, A. / Martinez, A.T. / Ruiz-Duenas, F.J.
History
DepositionAug 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VERSATILE PEROXIDASE VPL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7254
Polymers35,0281
Non-polymers6973
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.820, 64.220, 95.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VERSATILE PEROXIDASE VPL2 / VERSATILE LIQUID PHASE PEROXIDASE 2 / VERSATILE PEROXIDASE


Mass: 35028.492 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-361 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLEUROTUS ERYNGII (fungus) / Strain: IJFM, A169 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: O94753, 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.: 449 / Source method: isolated from a natural source / Formula: H2O

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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: 47.96 % / Description: NONE
Crystal growDetails: 10 % PEG 4000, 20% 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2014
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: 135701 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 11.98 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 6 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.2 / % possible all: 86.7

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Processing

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

3fmu


Resolution: 1.095→27.41 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1441 2000 1.5 %
Rwork0.1335 --
obs0.1337 135667 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.095→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 45 449 2852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012469
X-RAY DIFFRACTIONf_angle_d1.4543365
X-RAY DIFFRACTIONf_dihedral_angle_d14.191890
X-RAY DIFFRACTIONf_chiral_restr0.088366
X-RAY DIFFRACTIONf_plane_restr0.009449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0953-1.12270.29171090.29237333X-RAY DIFFRACTION76
1.1227-1.1530.2651370.23199059X-RAY DIFFRACTION94
1.153-1.1870.20311440.1889638X-RAY DIFFRACTION100
1.187-1.22530.18511450.16629694X-RAY DIFFRACTION100
1.2253-1.26910.16881440.15419644X-RAY DIFFRACTION100
1.2691-1.31990.15251450.13489702X-RAY DIFFRACTION100
1.3199-1.37990.14781450.12499678X-RAY DIFFRACTION100
1.3799-1.45270.13751450.11269721X-RAY DIFFRACTION100
1.4527-1.54370.12661460.10489722X-RAY DIFFRACTION100
1.5437-1.66290.1211460.10239757X-RAY DIFFRACTION100
1.6629-1.83020.10551460.11479795X-RAY DIFFRACTION100
1.8302-2.09490.14841470.12819799X-RAY DIFFRACTION100
2.0949-2.63910.13921480.13139931X-RAY DIFFRACTION100
2.6391-27.41860.14081530.136210194X-RAY DIFFRACTION100

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