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6a6q

Crystal structure of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH

Method: X-RAY DIFFRACTION Dmax: 66.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ligninase H8

Phanerochaete chrysosporium RP-78

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 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

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 6A6Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B80 REC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED Deposited 1999-02-03 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） 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
1B80 REC. LIGNIN PEROXIDASE H8 OXIDATIVELY PROCESSED Deposited 1999-02-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–372（345 aa） 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
1B82 PRISTINE RECOMB. LIGNIN PEROXIDASE H8 Deposited 1999-02-04 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 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 ligand/ion 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 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） 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 construct Different mutation/modification Different ligand/ion 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
6ISS Lignin peroxidase H8 triple mutant S49C/A67C/H239 Deposited 2018-11-19 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：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 mutation/modification Different ligand/ion 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 8 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 1–351； UniProt 22–372

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 6a6q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a6q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6a6q
Deposition date deposition_date2018-06-29
Structure title titleCrystal structure of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH
Keywords keywordsperoxidase, OXIDOREDUCTASE, heme binding domain; 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_guinier20.61 Å
Radius of gyration Rg (electron density) rg_electron19.47 Å
Forward intensity I(0) i024991600.00
Molecular weight molecular_weight37940.0 kDa
Excluded volume excluded_volume47147 ų
Envelope volume envelope_volume52886 ų
Hydration-shell volume shell_volume22262 ų
Envelope diameter envelope_diameter66.2 Å
Shell Rg shell_rg26.41 Å
Envelope Rg envelope_rg19.86 Å
Shape Rg shape_rg19.44 Å
Total Rg total_rg20.42 Å
Total atoms total_atoms2668
Residues n_residues343
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 dmax66.5 Å
Rg (real space) rg_real20.50 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real2.4990e+07
I(0) uncertainty (real space) i0_real_error3.1780e+05
Rg (reciprocal space) rg_reciprocal20.52 Å
I(0) (reciprocal space) i0_reciprocal24990000.0000
Solution quality estimate total_estimate0.7489
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0 Å
Skewness Skewness skewness0.196
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6158000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 0.387; Positv: 1.000; Valcen: 0.997; Smooth: 0.987
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6a6qa_
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 (2 domains)

Domain ID domain_id6a6qA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily10 —
Domain ID domain_id6a6qA02
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 (1)

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9. Files and Curves (10)