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- PDB-1b82: PRISTINE RECOMB. LIGNIN PEROXIDASE H8 -

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Basic information

Entry
Database: PDB / ID: 1b82
TitlePRISTINE RECOMB. LIGNIN PEROXIDASE H8
ComponentsPROTEIN (LIGNIN PEROXIDASE)
KeywordsOXIDOREDUCTASE / LIGNIN DEGRADATION / HEME / RADICAL REACTION / ELECTRON TRANSFER
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 / 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 / Ligninase H8
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBlodig, W. / Doyle, W.A. / Smith, A.T. / Piontek, K.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications ...Title: Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism.
Authors: Blodig, W. / Smith, A.T. / Doyle, W.A. / Piontek, K.
#1: Journal: Biochemistry / Year: 1998
Title: Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis.
Authors: Doyle, W.A. / Blodig, W. / Veitch, N.C. / Piontek, K. / Smith, A.T.
#2: Journal: Biochemistry / Year: 1998
Title: Autocatalytic formation of a hydroxy group at C beta of trp171 in lignin peroxidase.
Authors: Blodig, W. / Doyle, W.A. / Smith, A.T. / Winterhalter, K. / Choinowski, T. / Piontek, K.
#3: Journal: Biochem.J. / Year: 1996
Title: Expression of lignin peroxidase H8 in Escherichia coli: folding and activation of the recombinant enzyme with Ca2+ and haem.
Authors: Doyle, W.A. / Smith, A.T.
History
DepositionFeb 4, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 9, 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 / struct_conn / 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_asym_id / _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_asym_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_asym_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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: PROTEIN (LIGNIN PEROXIDASE)
B: PROTEIN (LIGNIN PEROXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3558
Polymers74,9612
Non-polymers1,3936
Water9,872548
1
A: PROTEIN (LIGNIN PEROXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1774
Polymers37,4811
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (LIGNIN PEROXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1774
Polymers37,4811
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.260, 94.420, 228.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.258, -0.966, -0.008), (0.966, 0.258), (0.002, -0.007, 1)
Vector: 35.593, 8.6, 57.8)

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Components

#1: Protein PROTEIN (LIGNIN PEROXIDASE) / E.C.1.11.1.14


Mass: 37480.719 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
Source method: isolated from a genetically manipulated source
Details: HEME CONTAINING / Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: BKM 1767 / Description: RECOMBINANT EXPRESSION IN E. COLI / Gene: LIP H8 / Variant: WILD TYPE / Plasmid: PFLAG1-LIPP / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P06181, lignin peroxidase
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 3.5 / Details: pH 3.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2ORCINOL11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMsodium succinate1drop
317 %(w/v)PEG60001reservoir
44 mM3,5-dihydroxytoluene1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 69484 / % possible obs: 94.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 4.3 / % possible all: 89.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 234766
Reflection shell
*PLUS
% possible obs: 89.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B80

1b80


Resolution: 1.8→30 Å / SU B: 2.16 / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPIC SCALING (REFMAC) WAS USED TO ACCOUNT FOR CRYSTAL ANISOTROPICITY PRISTINE LIGNIN PEROXIDASE HAS NOT REACTED WITH PEROXIDES. CRYSTALLISATION AND DATA COLLECTION WERE DONE IN THE ...Details: ANISOTROPIC SCALING (REFMAC) WAS USED TO ACCOUNT FOR CRYSTAL ANISOTROPICITY PRISTINE LIGNIN PEROXIDASE HAS NOT REACTED WITH PEROXIDES. CRYSTALLISATION AND DATA COLLECTION WERE DONE IN THE PRESENCE OF THE PHENOLIC ANTIOXIDANT ORCINOL.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 -5 %RANDOM
Rwork0.163 ---
all-69466 --
obs-69466 94.6 %-
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5224 0 92 548 5864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.482
X-RAY DIFFRACTIONp_mcangle_it2.23
X-RAY DIFFRACTIONp_scbond_it1.952
X-RAY DIFFRACTIONp_scangle_it3.133
X-RAY DIFFRACTIONp_plane_restr0.0210.3
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor12.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.3
X-RAY DIFFRACTIONp_chiral_restr0.150.13
X-RAY DIFFRACTIONp_mcbond_it21.48
X-RAY DIFFRACTIONp_scbond_it21.95
X-RAY DIFFRACTIONp_mcangle_it32.2
X-RAY DIFFRACTIONp_scangle_it33.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.254 / Rfactor obs: 0.189

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