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- PDB-1b80: REC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED -

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Basic information

Entry
Database: PDB / ID: 1b80
TitleREC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED
ComponentsPROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)
KeywordsOXIDOREDUCTASE / LIGNIN DEGRADATION / HEME / RADICAL REACTION / ELECTRON TRANSFER / AUTOCATALYTIC SELF-OXIDATION / BETA-HYDROXY TRYPTOPHAN
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: 1.73 Å
AuthorsBlodig, W. / Smith, A.T. / Doyle, W.A. / 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: J.Mol.Biol. / Year: 1999
Title: The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle.
Authors: Choinowski, T. / Blodig, W. / Winterhalter, K.H. / Piontek, K.
#2: 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.
#3: 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.
History
DepositionFeb 3, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 9, 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 / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)
B: PROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3878
Polymers74,9932
Non-polymers1,3936
Water10,323573
1
A: PROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1934
Polymers37,4971
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1934
Polymers37,4971
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.480, 94.930, 230.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2535, -0.96733, 0.00199), (0.96733, 0.25351, 0.00044), (-0.00093, 0.00181, 1)
Vector: 35.86729, 8.95346, 58.37613)

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Components

#1: Protein PROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)


Mass: 37496.719 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
Source method: isolated from a genetically manipulated source
Details: HEME CONTAINING, TRP171 IS HYDROXYLATED AT ITS CBETA ATOM
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.: 573 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS OXIDATIVELY PROCESSED ENZYME WAS OBTAINED BY TREATMENT OF THE PRISTINE RECOMBINANT AND ...THIS OXIDATIVELY PROCESSED ENZYME WAS OBTAINED BY TREATMENT OF THE PRISTINE RECOMBINANT AND REFOLDED ENZYME WITH 3 EQUIVALENTS OF HYDROGEN PEROXIDE PRIOR TO CRYSTALLISATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 3.5 / Details: 17 % PEG 6000 PH 3.5
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

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.73→20 Å / Num. obs: 79369 / % possible obs: 94.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.2
Reflection shellResolution: 1.73→1.79 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 391636
Reflection shell
*PLUS
% possible obs: 91.1 %

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Processing

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

1llp


Resolution: 1.73→20 Å / SU B: 1.98 / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPIC SCALING (REFMAC) WAS USED TO ACCOUNT FOR CRYSTAL ANISOTROPICITY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 -5 %RANDOM
Rwork0.17 ---
obs-79344 94.4 %-
Displacement parametersBiso mean: 22.1 Å2
Refinement stepCycle: LAST / Resolution: 1.73→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5227 0 92 573 5892
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_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3922
X-RAY DIFFRACTIONp_mcangle_it2.13
X-RAY DIFFRACTIONp_scbond_it1.8832
X-RAY DIFFRACTIONp_scangle_it2.963
X-RAY DIFFRACTIONp_plane_restr0.0210.3
X-RAY DIFFRACTIONp_chiral_restr0.1190.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1220.3
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor12.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.1 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_restr0.15
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it32.1
X-RAY DIFFRACTIONp_scangle_it32.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.289 / Rfactor obs: 0.219

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