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

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Basic information

Entry
Database: PDB / ID: 5abq
TitleCRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM PLEUROTUS ERYNGII. MUTANT VPi-SS. MUTATED RESIDUES T2K, A49C, A61C, D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R,A309K AND A314R.
ComponentsVERSATILE PEROXIDASE
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: 2.293 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8246
Polymers35,0481
Non-polymers7775
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.915, 68.763, 87.818
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


Mass: 35047.535 Da / Num. of mol.: 1 / 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.08 Å3/Da / Density % sol: 40.87 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CITRATE BUFFER AT PH 5.4, 12% PEG 4000 AND 0.2 M CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / 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: 2.3→50 Å / Num. obs: 12985 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 37.68 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.9
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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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: 2.293→43.909 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 34.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3004 1295 10.01 %
Rwork0.248 --
obs0.2532 12942 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.293→43.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 47 65 2427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032425
X-RAY DIFFRACTIONf_angle_d0.7723311
X-RAY DIFFRACTIONf_dihedral_angle_d14.653860
X-RAY DIFFRACTIONf_chiral_restr0.03362
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2926-2.38430.37591370.31691238X-RAY DIFFRACTION99
2.3843-2.49290.39441410.29571267X-RAY DIFFRACTION99
2.4929-2.62430.35031410.29861272X-RAY DIFFRACTION100
2.6243-2.78870.37121420.29381279X-RAY DIFFRACTION100
2.7887-3.00390.3281440.26981292X-RAY DIFFRACTION100
3.0039-3.30610.29111440.25581295X-RAY DIFFRACTION100
3.3061-3.78430.30061440.24081297X-RAY DIFFRACTION100
3.7843-4.76690.25631460.22331317X-RAY DIFFRACTION100
4.7669-43.9170.27531560.22161390X-RAY DIFFRACTION99
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)
14.38490.6094-0.78494.4781-1.53130.98560.50050.88170.2295-1.2490.1807-0.2406-0.76530.5321-0.22141.0149-0.01790.25220.5343-0.01410.5388-18.32616.41113.6129
22.4443-2.0763-0.24975.78040.07933.3584-0.1515-0.1356-0.4378-0.55150.1113-0.4845-0.37690.31550.10520.23370.02350.0890.3048-0.05820.3434-18.12311.047320.8276
34.0413-0.346-2.94485.84821.91314.76680.05220.1080.6746-1.16580.0372-0.4296-0.35250.356-0.14240.48440.01350.07450.27990.0130.3097-17.92479.951815.6332
41.39780.4871-0.50655.28190.02991.87080.005-0.06190.2604-0.34020.0848-0.34550.02050.1135-0.08450.22450.00050.04290.2376-0.03770.3074-16.885-6.973916.8976
52.7442.06680.08593.40011.39753.3950.3668-0.0160.20480.06810.065-1.55480.33630.3501-0.30860.45290.03590.17840.6191-0.13431.11630.9058-9.764117.3729
63.6110.35711.04593.2767-0.77391.2184-0.4329-0.0636-0.1512-0.45380.0947-1.4981-0.43990.30220.23010.42110.01940.2630.3985-0.07521.0484-4.4629-16.380517.4509
73.4941-0.57-0.44722.38281.30772.6762-0.58440.4319-0.0593-0.40730.04980.7133-0.4132-0.4076-0.4661.00010.0515-0.26490.4469-0.07810.2899-21.3917-3.59595.2985
80.8885-0.0821-0.73880.48150.36790.91180.19180.4495-0.5547-0.2198-0.0508-0.68890.08110.2536-0.27120.90660.1160.36510.6165-0.10821.2979-0.1245-12.67546.203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 28 THROUGH 81 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 82 THROUGH 113 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 114 THROUGH 180 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 181 THROUGH 212 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 213 THROUGH 250 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 251 THROUGH 278 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 279 THROUGH 314 )

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