SAXSdb — 1c89

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

ANTIFREEZE PROTEIN TYPE III

Pachycara brachycephalum

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 1–134	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.7；277 K；Pressure 1 NMR sample composition：90% H2O/10% D2O	Resolution not provided

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 1C89	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C8A NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES Deposited 2000-05-04	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–134（134 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；277 K；Pressure 1 NMR sample composition 90% H2O/10% D2O	Resolution not provided
3NLA NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, 40 STRUCTURES Deposited 1998-02-24	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–73（73 aa） Fragment：N-TERMINAL DOMAIN WITH A LINKER PORTION	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；277 K	Resolution not provided
3RDN NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, MINIMIZED AVERAGE STRUCTURE Deposited 1998-02-24	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–73（73 aa） Fragment：N-TERMINAL DOMAIN WITH A LINKER PORTION	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；277 K	Resolution not provided

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANP3_RHIDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 1–134

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	1c89
Deposition date deposition_date	2000-05-04
Structure title title	NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES
Keywords keywords	ANTIFREEZE, THERMAL HYSTERESIS PROTEIN, ICE BINDING PROTEIN, ANTIFREEZE PROTEIN; ANTIFREEZE PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.84 Å
Radius of gyration Rg (electron density) rg_electron	16.25 Å
Forward intensity I(0) i0	4292590000.00
Molecular weight molecular_weight	579080.0 kDa
Excluded volume excluded_volume	734380 Å³
Envelope volume envelope_volume	34976 Å³
Hydration-shell volume shell_volume	16783 Å³
Envelope diameter envelope_diameter	60.7 Å
Shell Rg shell_rg	23.63 Å
Envelope Rg envelope_rg	18.09 Å
Shape Rg shape_rg	16.23 Å
Total Rg total_rg	16.41 Å
Total atoms total_atoms	82720
Residues n_residues	5360
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	52.5 Å
Rg (real space) rg_real	15.92 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	4.2930e+09
I(0) uncertainty (real space) i0_real_error	4.8520e+07
Rg (reciprocal space) rg_reciprocal	15.91 Å
I(0) (reciprocal space) i0_reciprocal	4293000000.0000
Solution quality estimate total_estimate	0.7734
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.6 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.290
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	554300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.715; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c89a1
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.1 — AFP III-like domain
Family Family family	b.85.1.1 — AFP III-like domain

Domain ID domain_id	d1c89a2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.1 — AFP III-like domain
Family Family family	b.85.1.1 — AFP III-like domain

CATH v4.4 (2 domains)

Domain ID domain_id	1c89A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1210 — Type Iii Antifreeze Protein Isoform Hplc 12
Homologous superfamily homologous superfamily	10 — Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain

Domain ID domain_id	1c89A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1210 — Type Iii Antifreeze Protein Isoform Hplc 12
Homologous superfamily homologous superfamily	10 — Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain

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8. Citations (5)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	ANTIFREEZE PROTEIN TYPE III
Molecular weight formula_weight	14490.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	82720

来源生物 organism	Pachycara brachycephalum
NCBI Class编号 ncbi_taxonomy_id	36221
宿主生物 host_organism	Escherichia coli

NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES

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

ANTIFREEZE PROTEIN TYPE III

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (5)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/c8/1c89/1c89.fit
pddf	/app/data/pr_computation/c8/1c89/1c89.pr.out
profile	/app/data/saxs_computation/c8/1c89/1c89.dat