SAXSdb — 1hfu

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

LACCASE 1

COPRINUS CINEREUS

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 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 19–521	Not recorded	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CU COPPER (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；PROTEIN WAS AT 30MG/ML IN 100MM ACETATE BUFFER PH 5.5. CRYSTALS GROW FROM 20-30% PEG 8000	Resolution 1.68 Å R-free 0.207

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 1HFU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A65 TYPE-2 CU-DEPLETED LACCASE FROM COPRINUS CINEREUS Deposited 1998-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–522（504 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PYE TETRAHYDROPYRAN × 1 CU COPPER (II) ION × 3 O OXYGEN ATOM × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.23 Å R-free 0.220

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9Y780
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–503； UniProt 19–521

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hfu
Deposition date deposition_date	2000-12-08
Structure title title	TYPE-2 CU-DEPLETED LACCASE FROM COPRINUS CINEREUS at 1.68 A resolution
Keywords keywords	OXIDOREDUCTASE, LACCASE, BLUE MULTI-COPPER OXIDASE, TYPE-2 COPPER DEPLETED, GLYCOPROTEIN; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.78 Å
Radius of gyration Rg (electron density) rg_electron	21.65 Å
Forward intensity I(0) i0	52441200.00
Molecular weight molecular_weight	55047.0 kDa
Excluded volume excluded_volume	68145 Å³
Envelope volume envelope_volume	77379 Å³
Hydration-shell volume shell_volume	28533 Å³
Envelope diameter envelope_diameter	73.0 Å
Shell Rg shell_rg	29.61 Å
Envelope Rg envelope_rg	21.94 Å
Shape Rg shape_rg	21.64 Å
Total Rg total_rg	22.54 Å
Total atoms total_atoms	3880
Residues n_residues	500
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

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

Maximum dimension Dmax dmax	70.6 Å
Rg (real space) rg_real	22.64 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	5.2440e+07
I(0) uncertainty (real space) i0_real_error	6.7000e+05
Rg (reciprocal space) rg_reciprocal	22.67 Å
I(0) (reciprocal space) i0_reciprocal	52440000.0000
Solution quality estimate total_estimate	0.8190
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.426
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11650000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	LACCASE 1
Molecular weight formula_weight	54409.3 kDa
EC 编号 ec_number	1.10.3.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4358

AIVNSVDTMTLTNANVSPDGFTRAGILVNGVHGPLIRGGKNDNFELNVVNDLDNPTMLRPTSIHWHGLFQRGTNWADGADGVNQCPISPGHAFLYKFTPAGHAGTFWYHSHFGTQYCDGLRGPMVIYDDNDPHAALYDEDDENTIITLADWYHIPAPSIQGAAQPDATLINGKGRYVGGPAAELSIVNVEQGKKYRMRLISLSCDPNWQFSIDGHELTIIEVDGELTEPHTVDRLQIFTGQRYSFVLDANQPVDNYWIRAQPNKGRNGLAGTFANGVNSAILRYAGAANADPTTSANPNPAQLNEADLHALIDPAAPGIPTPGAADVNLRFQLGFSGGRFTINGTAYESPSVPTLLQIMSGAQSANDLLPAGSVYELPRNQVVELVVPAGVLGGPHPFHLHGHAFSVVRSAGSSTYNFVNPVKRDVVSLGVTGDEVTIRFVTDNPGPWFFHCHIEFHLMNGLAIVFAEDMANTVDANNPPVEWAQLCEIYDDLPPEATSIQTV

来源 Source

来源生物 organism	COPRINUS CINEREUS
通用名 common_name	INKY CAP FUNGUS
NCBI Class编号 ncbi_taxonomy_id	5346
宿主生物 host_organism	ASPERGILLUS ORYZAE

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	461

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1hfua1
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1hfua2
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1hfua3
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.3 — Multidomain cupredoxins

Domain ID domain_id	d1hfua4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	1hfuA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1hfuA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1hfuA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (3)

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Unit-cell length a length_a	45.120 Å
Unit-cell length b length_b	84.560 Å
Unit-cell length c length_c	139.030 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1840
R_free r_free	0.2075

fit	/app/data/saxs_computation/hf/1hfu/1hfu.fit
pddf	/app/data/pr_computation/hf/1hfu/1hfu.pr.out
profile	/app/data/saxs_computation/hf/1hfu/1hfu.dat

TYPE-2 CU-DEPLETED LACCASE FROM COPRINUS CINEREUS at 1.68 A resolution

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

LACCASE 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction