SAXSdb — 1ck4

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

INTEGRIN ALPHA-1

Rattus norvegicus

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 167–364	Fragment：I-DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.299
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 167–364	Fragment：I-DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.299

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 1CK4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MHP Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody Deposited 2002-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 169–360（192 aa） Fragment：alpha1 I-domain	Mutation：G217V, R218Q, Q219R, L222R	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 1500, Tris, NaCl, beta-mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.80 Å R-free 0.272
1MHP Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody Deposited 2002-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 169–360（192 aa） Fragment：alpha1 I-domain	Mutation：G217V, R218Q, Q219R, L222R	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 1500, Tris, NaCl, beta-mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.80 Å R-free 0.272
2B2X VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 151–364（214 aa） Fragment：I domain R delta H	Mutation：G217V, R218Q, Q219R, L222R	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Peg 20K, Mes, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.272
2B2X VLA1 RdeltaH I-domain complexed with a quadruple mutant of the AQC2 Fab Deposited 2005-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 151–364（214 aa） Fragment：I domain R delta H	Mutation：G217V, R218Q, Q219R, L222R	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；Peg 20K, Mes, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.272

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

View Construct and Data Evidence

UniProt name	ITA1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–198； UniProt 167–364 Author chain B； PDBConstruct 1–198； UniProt 167–364

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ck4
Deposition date deposition_date	1999-04-27
Structure title title	CRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN.
Keywords keywords	I-DOMAIN, METAL BINDING, COLLAGEN, ADHESION, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	25.30 Å
Radius of gyration Rg (electron density) rg_electron	24.86 Å
Forward intensity I(0) i0	31421800.00
Molecular weight molecular_weight	43205.0 kDa
Excluded volume excluded_volume	54154 Å³
Envelope volume envelope_volume	63641 Å³
Hydration-shell volume shell_volume	22554 Å³
Envelope diameter envelope_diameter	88.8 Å
Shell Rg shell_rg	30.58 Å
Envelope Rg envelope_rg	24.92 Å
Shape Rg shape_rg	24.86 Å
Total Rg total_rg	25.51 Å
Total atoms total_atoms	3753
Residues n_residues	388
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	85.8 Å
Rg (real space) rg_real	26.30 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.1350e+07
I(0) uncertainty (real space) i0_real_error	3.2680e+05
Rg (reciprocal space) rg_reciprocal	25.42 Å
I(0) (reciprocal space) i0_reciprocal	31420000.0000
Solution quality estimate total_estimate	0.6355
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	24.5 Å
Skewness Skewness skewness	0.527
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	5.7720
Highest regularization parameter α highest_alpha	9391000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.703; Stabil: 0.902; Sysdev: 0.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.699

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ck4a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.1 — Integrin A (or I) domain

Domain ID domain_id	d1ck4b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.1 — Integrin A (or I) domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ck4A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	1ck4B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

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8. Citations (1)

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Unit-cell length a length_a	34.770 Å
Unit-cell length b length_b	85.920 Å
Unit-cell length c length_c	132.560 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.2340
R_free r_free	0.2990

Description description	INTEGRIN ALPHA-1
Molecular weight formula_weight	22118.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3968

CRYSTAL STRUCTURE OF RAT A1B1 INTEGRIN I-DOMAIN.

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

INTEGRIN ALPHA-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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

fit	/app/data/saxs_computation/ck/1ck4/1ck4.fit
pddf	/app/data/pr_computation/ck/1ck4/1ck4.pr.out
profile	/app/data/saxs_computation/ck/1ck4/1ck4.dat