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- PDB-4fdq: The crystal structures of several mutants of pleurotus eryngii ve... -

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Basic information

Entry
Database: PDB / ID: 4fdq
TitleThe crystal structures of several mutants of pleurotus eryngii versatile peroxidase
ComponentsVersatile peroxidase VPL2
KeywordsOXIDOREDUCTASE / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / AROMATIC-SUBSTRATE BINDING
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: 1.6 Å
AuthorsMate, M.J. / Romero, A. / Ruiz-Duenas, F.J. / Martinez, A.T.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Two Oxidation Sites for Low Redox Potential Substrates: A DIRECTED MUTAGENESIS, KINETIC, AND CRYSTALLOGRAPHIC STUDY ON PLEUROTUS ERYNGII VERSATILE PEROXIDASE.
Authors: Morales, M. / Mate, M.J. / Romero, A. / Martinez, M.J. / Martinez, A.T. / Ruiz-Duenas, F.J.
#1: Journal: 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.T. / Martinez, A.T.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,1237
Polymers33,1461
Non-polymers9776
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.230, 96.230, 98.730
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-705-

HOH

21A-761-

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: 33146.113 Da / Num. of mol.: 1 / Fragment: UNP residues 31-349 / Mutation: E140G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) pleurotus eryngii (fungus) / Gene: vpl2 / Production host: Escherichia coli (E. coli) / References: UniProt: O94753, versatile peroxidase

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Non-polymers , 5 types, 392 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.4 M ammonium sulfate, 0.1 M sodium cacodilate and 2% 1,3-propanediol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 20, 2007
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→48.12 Å / Num. all: 59138 / Num. obs: 57998 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 13.182 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.2 / Num. unique all: 8340 / % possible all: 97.1

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VKA

2vka


Resolution: 1.6→48.12 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.107 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17945 2944 5.1 %RANDOM
Rwork0.15255 ---
all0.159 59138 --
obs0.15392 55052 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.316 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 62 386 2777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222464
X-RAY DIFFRACTIONr_angle_refined_deg2.3422.0143378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6825.192104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31315351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1631510
X-RAY DIFFRACTIONr_chiral_restr0.1870.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0221927
X-RAY DIFFRACTIONr_mcbond_it1.3031.51587
X-RAY DIFFRACTIONr_mcangle_it2.12422549
X-RAY DIFFRACTIONr_scbond_it3.1713877
X-RAY DIFFRACTIONr_scangle_it4.7844.5829
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 201 -
Rwork0.235 4014 -
obs-4014 96.92 %

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