SAXSdb — 1c8i

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (PEROXIDASE)

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–364	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BMA beta-D-mannopyranose × 1 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HOA HYDROXYAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；pH 5.6	Resolution 2.00 Å R-free 0.223

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 1C8I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ARP Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 angstroms resolution: structural comparisons with the lignin and cytochrome C peroxidases Deposited 1993-06-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1ARU CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS Deposited 1995-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CYN CYANIDE ION × 1 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.60 Å
1ARV CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS Deposited 1995-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CYN CYANIDE ION × 1 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 1.60 Å
1ARW CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS Deposited 1995-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CYN CYANIDE ION × 1 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；pH 4.0	Resolution 1.60 Å
1ARX CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS Deposited 1995-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CA CALCIUM ION × 2 IOD IODIDE ION × 7 K POTASSIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.90 Å
1ARY CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS Deposited 1995-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CA CALCIUM ION × 2 IOD IODIDE ION × 7 K POTASSIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 1.90 Å
1CK6 BINDING MODE OF SALICYLHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE Deposited 1999-04-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–364（329 aa）	Not recorded	BMA beta-D-mannopyranose × 1 CA CALCIUM ION × 2 SHA SALICYLHYDROXAMIC ACID × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.90 Å R-free 0.228
1GZA PEROXIDASE Deposited 1996-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CA CALCIUM ION × 2 IOD IODIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.06 Å
1GZB PEROXIDASE Deposited 1996-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.80 Å
1HSR BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE Deposited 1997-07-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 BHO BENZHYDROXAMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 1.60 Å
2E39 Crystal structure of the CN-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution Deposited 2006-11-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 CA CALCIUM ION × 2 CYN CYANIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；297 K；37% saturated ammonium sulfate, Tris-HCl, pH 7.5, MICRODIALYSIS, temperature 297K	Resolution 1.30 Å R-free 0.203
2E3A Crystal structure of the NO-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution Deposited 2006-11-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NO NITRIC OXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；297 K；37% saturated ammonium sulfate, Tris-HCl, pH 7.5, MICRODIALYSIS, temperature 297K	Resolution 1.30 Å R-free 0.201
2E3B Crystal structure of the HA-bound form of Arthromyces ramosus peroxidase at 1.3 Angstroms resolution Deposited 2006-11-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–364（344 aa）	Not recorded	MAN alpha-D-mannopyranose × 1 CA CALCIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HOA HYDROXYAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；297 K；37% saturated ammonium sulfate, Tris-HCl, pH 7.5, MICRODIALYSIS, temperature 297K	Resolution 1.30 Å R-free 0.199

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PER_ARTRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–344； UniProt 21–364

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c8i
Deposition date deposition_date	2000-05-08
Structure title title	BINDING MODE OF HYDROXYLAMINE TO ARTHROMYCES RAMOSUS PEROXIDASE
Keywords keywords	OXIDOREDUCTASE, GLYCOPROTEIN, PEROXIDASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.51 Å
Radius of gyration Rg (electron density) rg_electron	19.43 Å
Forward intensity I(0) i0	23971500.00
Molecular weight molecular_weight	36419.0 kDa
Excluded volume excluded_volume	45080 Å³
Envelope volume envelope_volume	50109 Å³
Hydration-shell volume shell_volume	21425 Å³
Envelope diameter envelope_diameter	63.6 Å
Shell Rg shell_rg	26.13 Å
Envelope Rg envelope_rg	19.68 Å
Shape Rg shape_rg	19.43 Å
Total Rg total_rg	20.28 Å
Total atoms total_atoms	2551
Residues n_residues	336
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	64.8 Å
Rg (real space) rg_real	20.43 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	2.3970e+07
I(0) uncertainty (real space) i0_real_error	2.8330e+05
Rg (reciprocal space) rg_reciprocal	20.44 Å
I(0) (reciprocal space) i0_reciprocal	23970000.0000
Solution quality estimate total_estimate	0.7110
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	6076000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.995; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PEROXIDASE)
Molecular weight formula_weight	35722.8 kDa
EC 编号 ec_number	1.11.1.7
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2759

QGPGGGGGSVTCPGGQSTSNSQCCVWFDVLDDLQTNFYQGSKCESPVRKILRIVFHDAIGFSPALTAAGQFGGGGADGSIIAHSNIELAFPANGGLTDTIEALRAVGINHGVSFGDLIQFATAVGMSNCPGSPRLEFLTGRSNSSQPSPPSLIPGPGNTVTAILDRMGDAGFSPDEVVDLLAAHSLASQEGLNSAIFRSPLDSTPQVFDTQFYIETLLKGTTQPGPSLGFAEELSPFPGEFRMRSDALLARDSRTACRWQSMTSSNEVMGQRYRAAMAKMSVLGFDRNALTDCSDVIPSAVSNNAAPVIPGGLTVDDIEVSCPSEPFPEIATASGPLPSLAPAP

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	HYDROXYAMINE
Molecular weight formula_weight	33.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c8ia_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

CATH v4.4 (2 domains)

Domain ID domain_id	1c8iA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1c8iA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

▶

8. Citations (7)

;Direct binding of hydroxylamine to the heme iron of Arthromyces ramosus peroxidase. Substrate analogue that inhibits compound I formation in a competetive manner. ;

J.Biol.Chem. (2000)

PMID: 10915789 · DOI: 10.1074/jbc.M004223200 PRIMARY

;Binding Mode of Benzhydroxamic Acid to Arthromyces Ramosus Peroxidase Shown by X-Ray Crystallographic Analysis of the Complex at 1.6 A Resolution ;

FEBS Lett. (1997)

DOI: 10.1016/S0014-5793(97)00751-5

;Binding of Iodide to Arthromyces Ramosus Peroxidase Investigated with X-Ray Crystallographic Analysis, 1H and 127I NMR Spectroscopy, and Steady-State Kinetics ;

J.Biol.Chem. (1997)

DOI: 10.1074/jbc.272.9.5752

Pentacoordination of the Heme Iron of Arthromyces Ramosus Peroxidase Shown by a 1.8 A Resolution Crystallographic Study at Ph 4.5

FEBS Lett. (1996)

DOI: 10.1016/0014-5793(95)01458-6

;Crystal Structures of Cyanide-and Triiodide-Bound Forms of Arthromyces Ramosus Peroxidase at Different Ph Values. Perturbations of Active Site Residues and Their Implication in Enzyme Catalysis ;

J.Biol.Chem. (1995)

DOI: 10.1074/jbc.270.37.21884

;Crystal Structure of the Fungal Peroxidase from Arthromyces Ramosus at 1.9 A Resolution. Structural Comparisons with the Lignin and Cytochrome C Peroxidases ;

J.Mol.Biol. (1994)

Crystallization and Preliminary X-Ray Diffraction Studies of Peroxidase from a Fungus Arthromyces Ramosus

Proteins (1993)

▶

Unit-cell length a length_a	74.400 Å
Unit-cell length b length_b	74.400 Å
Unit-cell length c length_c	117.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1620
R_work r_work	0.1620
R_free r_free	0.2230

fit	/app/data/saxs_computation/c8/1c8i/1c8i.fit
pddf	/app/data/pr_computation/c8/1c8i/1c8i.pr.out
profile	/app/data/saxs_computation/c8/1c8i/1c8i.dat

BINDING MODE OF HYDROXYLAMINE TO ARTHROMYCES RAMOSUS PEROXIDASE