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- PDB-6iss: Lignin peroxidase H8 triple mutant S49C/A67C/H239 -

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Basic information

Entry
Database: PDB / ID: 6iss
TitleLignin peroxidase H8 triple mutant S49C/A67C/H239
ComponentsLigninase H8
KeywordsOXIDOREDUCTASE / peroxidase / heme binding domain
Function / homology
Function and homology information


lignin peroxidase / diarylpropane peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / 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 / Ligninase H8
Similarity search - Component
Biological speciesPhanerochaete chrysosporium RP-78 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsSeo, H. / Son, H. / Kim, K.-J.
CitationJournal: Enzyme.Microb.Technol. / Year: 2021
Title: Extra disulfide and ionic salt bridge improves the thermostability of lignin peroxidase H8 under acidic condition
Authors: Son, H. / Seo, H. / Han, S. / Kim, S. / Thanh, L. / Khan, M. / Sung, H. / Kang, S.H. / Kim, K.J. / Kim, Y.
History
DepositionNov 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ligninase H8
G: Ligninase H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4658
Polymers75,0722
Non-polymers1,3936
Water10,215567
1
A: Ligninase H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2324
Polymers37,5361
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-36 kcal/mol
Surface area13610 Å2
MethodPISA
2
G: Ligninase H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2324
Polymers37,5361
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-36 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.959, 93.740, 227.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11G-745-

HOH

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Components

#1: Protein Ligninase H8 / lignin peroxidase H8 / Diarylpropane peroxidase / Lignin peroxidase


Mass: 37535.816 Da / Num. of mol.: 2 / Mutation: S49C,A67C,H239E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium RP-78 (fungus)
Gene: LPOA / Plasmid: pET21b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06181, lignin peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / 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.: 567 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 17, 2018
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 115965 / % possible obs: 98.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.76
Reflection shellResolution: 1.53→1.56 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.39 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6Q

6a6q


Resolution: 1.53→29.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.413 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 5693 4.9 %RANDOM
Rwork0.1697 ---
obs0.1709 110231 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.55 Å2 / Biso mean: 14.865 Å2 / Biso min: 6.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2--0.54 Å20 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.53→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 90 567 5867
Biso mean--11.52 24.01 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174763
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.6767477
X-RAY DIFFRACTIONr_angle_other_deg1.5921.58511144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26224.642265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64915780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6371518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026286
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021080
LS refinement shellResolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 417 -
Rwork0.259 7846 -
all-8263 -
obs--96.15 %

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