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1b80

REC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED

Method: X-RAY DIFFRACTION Dmax: 123.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RECOMBINANT LIGNIN PEROXIDASE H8)

Phanerochaete chrysosporium

UniProt P06181

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 22–372 Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.5；17 % PEG 6000 PH 3.5 Resolution 1.73 Å R-free 0.208
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 28–372 Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 3.5；17 % PEG 6000 PH 3.5 Resolution 1.73 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1B80 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B82 PRISTINE RECOMB. LIGNIN PEROXIDASE H8 Deposited 1999-02-04 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–373（350 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
Not recorded CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；pH 3.5
Resolution 1.80 Å R-free 0.194
1B82 PRISTINE RECOMB. LIGNIN PEROXIDASE H8 Deposited 1999-02-04 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–373（350 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
Not recorded CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；pH 3.5
Resolution 1.80 Å R-free 0.194
1B85 LIGNIN PEROXIDASE Deposited 1999-02-05 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–372（351 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
Mutation：W171F SUBSTITUTION CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 1.85 Å R-free 0.181
1B85 LIGNIN PEROXIDASE Deposited 1999-02-05 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–372（351 aa） Fragment：MATURE PROTEIN PLUS 7-RESIDUE PROSEQUENCE
Mutation：W171F SUBSTITUTION CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 1.85 Å R-free 0.181
6A6Q Crystal structure of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH Deposited 2018-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–372（351 aa）
Mutation：A55R, N156E, H239E Non-standard monomer：Yes (specific site not provided by mmCIF) HEB HEME B/C × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；PEG 6000
Resolution 1.67 Å R-free 0.171
6ISS Lignin peroxidase H8 triple mutant S49C/A67C/H239 Deposited 2018-11-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–372（351 aa）
Mutation：S49C,A67C,H239E Non-standard monomer：Yes (specific site not provided by mmCIF) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 6000
Resolution 1.53 Å R-free 0.196
6ISS Lignin peroxidase H8 triple mutant S49C/A67C/H239 Deposited 2018-11-19 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 22–372（351 aa）
Mutation：S49C,A67C,H239E Non-standard monomer：Yes (specific site not provided by mmCIF) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 6000
Resolution 1.53 Å R-free 0.196

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LIG8_PHACH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–351； UniProt 22–372 Author chain B； PDBConstruct 7–351； UniProt 28–372

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1b80

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b80
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b80
Deposition date deposition_date1999-02-03
Structure title titleREC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED
Keywords keywords;LIGNIN DEGRADATION, HEME, RADICAL REACTION, ELECTRON TRANSFER, AUTOCATALYTIC SELF-OXIDATION, BETA-HYDROXY TRYPTOPHAN, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.36 Å
Radius of gyration Rg (electron density) rg_electron35.44 Å
Forward intensity I(0) i090400400.00
Molecular weight molecular_weight75531.0 kDa
Excluded volume excluded_volume93833 ų
Envelope volume envelope_volume116740 ų
Hydration-shell volume shell_volume29291 ų
Envelope diameter envelope_diameter125.7 Å
Shell Rg shell_rg38.89 Å
Envelope Rg envelope_rg35.26 Å
Shape Rg shape_rg35.43 Å
Total Rg total_rg35.73 Å
Total atoms total_atoms5315
Residues n_residues692
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax123.2 Å
Rg (real space) rg_real35.81 Å
Rg uncertainty (real space) rg_real_error1.13 Å
I(0) (real space) i0_real9.0400e+07
I(0) uncertainty (real space) i0_real_error1.6810e+06
Rg (reciprocal space) rg_reciprocal35.53 Å
I(0) (reciprocal space) i0_reciprocal90380000.0000
Solution quality estimate total_estimate0.7269
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.4 Å
Skewness Skewness skewness0.527
Kurtosis Kurtosis kurtosis-0.615
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23430000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.408; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.392; Smooth: 0.828
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b80a_
Class classa — All alpha proteins
Fold Fold folda.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamilya.93.1 — Heme-dependent peroxidases
Family Family familya.93.1.1 — CCP-like
Domain ID domain_idd1b80b_
Class classa — All alpha proteins
Fold Fold folda.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamilya.93.1 — Heme-dependent peroxidases
Family Family familya.93.1.1 — CCP-like

CATH v4.4 (4 domains)

Domain ID domain_id1b80A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1b80A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily10 — Peroxidase, domain 2
Domain ID domain_id1b80B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1b80B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily10 — Peroxidase, domain 2
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8. Citations (4)

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9. Files and Curves (10)