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- PDB-2vka: Site-Directed Mutagenesis of the Catalytic Tryptophan Environment... -

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Basic information

Entry
Database: PDB / ID: 2vka
TitleSite-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase
ComponentsVERSATILE PEROXIDASE VPL2
KeywordsOXIDOREDUCTASE / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / POLYVALENT PEROXIDASE / AROMATIC-SUBSTRATE BINDING / MN-INDEPENDENT OXIDATION
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 VPL2
Similarity search - Component
Biological speciesPLEUROTUS ERYNGII (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRuiz-Duenas, F.J. / Morales, M. / Mate, M.J. / Romero, A. / Martinez, M.J. / Smith, A. / Martinez, A.T.
CitationJournal: Biochemistry / Year: 2008
Title: Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus Eryngii Versatile Peroxidase
Authors: Ruiz-Duenas, F.J. / Morales, M. / Mate, M.J. / Romero, A. / Martinez, M.J. / Smith, A. / Martinez, A.T.
History
DepositionDec 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 13, 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)34,2196
Polymers33,3341
Non-polymers8855
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.290, 96.290, 98.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

21A-2051-

HOH

31A-2099-

HOH

41A-2266-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33334.273 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLEUROTUS ERYNGII (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O94753, versatile peroxidase

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Non-polymers , 5 types, 423 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 277 TO PHE
Has protein modificationY
Sequence detailsMUTATION M247F

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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: 2.9 Å3/Da / Density % sol: 63.9 % / Description: NONE
Crystal growDetails: 1.4 M AMMONIUM SULFATE AND 100 MM SODIUM CACODILATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→28.01 Å / Num. obs: 30110 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.15 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.72
Reflection shellResolution: 2→2.02 Å / Redundancy: 4.18 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.89 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0036refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOQ

2boq


Resolution: 2→26.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.948 / SU ML: 0.078 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1484 4.99 %RANDOM
Rwork0.144 ---
obs0.146 30108 99.3 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.341 Å20 Å20 Å2
2---0.341 Å20 Å2
3---0.683 Å2
Refinement stepCycle: LAST / Resolution: 2→26.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 56 418 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.0143407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02425.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3681510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21735
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7371.51640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13422566
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9173940
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8734.5839
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 8.48→26.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.187 21
Rwork0.173 374
Refinement TLS params.Method: refined / Origin x: 3.9644 Å / Origin y: 16.0208 Å / Origin z: -0.013 Å
111213212223313233
T-0.1189 Å20.0042 Å20.0153 Å2--0.1144 Å2-0.0082 Å2---0.0993 Å2
L0.6789 °20.1425 °20.165 °2-1.1514 °20.358 °2--0.9685 °2
S-0.0175 Å °-0.0356 Å °-0.0115 Å °0.0351 Å °-0.0017 Å °-0.0235 Å °0.0164 Å °0.0264 Å °0.0192 Å °

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