SAXSdb — 1a7b

▼

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

CD2

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–121 Chain B； UniProt 23–121 Chain C； UniProt 23–121 Chain D； UniProt 23–121	Fragment：DOMAIN 1 Mutation：DEL(M46, K47)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5	Resolution 3.10 Å R-free 0.306
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–121 Chain B； UniProt 23–121	Fragment：DOMAIN 1 Mutation：DEL(M46, K47)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5	Resolution 3.10 Å R-free 0.306
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 23–121 Chain D； UniProt 23–121	Fragment：DOMAIN 1 Mutation：DEL(M46, K47)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5	Resolution 3.10 Å R-free 0.306

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 1A7B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A64 ENGINEERING A MISFOLDED FORM OF RAT CD2 Deposited 1998-03-05	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–121（99 aa） Fragment：DOMAIN 1 Chain B 23–121（99 aa） Fragment：DOMAIN 1	Mutation：DEL(M46, K47) Mutation：DEL(M46, K47)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；20% MPD, 200MM NACL, 0.1M NACO, PH 4.6	Resolution 2.00 Å R-free 0.273
1A6P ENGINEERING OF A MISFOLDED FORM OF CD2 Deposited 1998-02-26	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–121（96 aa） Fragment：DOMAIN 1 Chain B 26–121（96 aa） Fragment：DOMAIN 1	Mutation：DEL(M46, K47) Mutation：DEL(M46, K47)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；20% PEG 4000, 5% GLYCEROL, 0.1M NACO, PH 4.6	Resolution 2.08 Å R-free 0.296
1CDC CD2, N-TERMINAL DOMAIN (1-99), TRUNCATED FORM Deposited 1995-05-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–121（99 aa） Chain B 23–121（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1HNG CRYSTAL STRUCTURE AT 2.8 ANGSTROMS RESOLUTION OF A SOLUBLE FORM OF THE CELL ADHESION MOLECULE CD2 Deposited 1994-08-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–198（176 aa） Chain B 23–198（176 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1T6W RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES Deposited 2004-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–121（99 aa）	Mutation：N15D, N17D	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure 1 NMR sample composition 95% H2O, 5% D2O, protein 1 mM, KCl 130 mM, CaCl2 10 mM, PIPES 20 mM \| 95% H2O/5% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 23–121 Author chain B； PDBConstruct 1–97； UniProt 23–121 Author chain C； PDBConstruct 1–97； UniProt 23–121 Author chain D； PDBConstruct 1–97； UniProt 23–121

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	1a7b
Deposition date deposition_date	1998-03-10
Structure title title	ENGINEERING A MISFOLDED FORM OF CD2
Keywords keywords	CD2, DOMAIN SWAPPING, OLIGOMERIZATION, PROTEIN FOLDING, PROTEIN EVOLUTION; DOMAIN SWAPPING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.73 Å
Radius of gyration Rg (electron density) rg_electron	21.71 Å
Forward intensity I(0) i0	29767000.00
Molecular weight molecular_weight	41872.0 kDa
Excluded volume excluded_volume	52592 Å³
Envelope volume envelope_volume	64218 Å³
Hydration-shell volume shell_volume	24733 Å³
Envelope diameter envelope_diameter	78.9 Å
Shell Rg shell_rg	28.56 Å
Envelope Rg envelope_rg	21.75 Å
Shape Rg shape_rg	21.70 Å
Total Rg total_rg	22.66 Å
Total atoms total_atoms	2956
Residues n_residues	372
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	74.4 Å
Rg (real space) rg_real	22.60 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.9770e+07
I(0) uncertainty (real space) i0_real_error	3.7630e+05
Rg (reciprocal space) rg_reciprocal	22.63 Å
I(0) (reciprocal space) i0_reciprocal	29770000.0000
Solution quality estimate total_estimate	0.5977
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.156
Kurtosis Kurtosis kurtosis	-0.299
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8995000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 0.999; Sysdev: 0.130; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a7ba_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1a7bb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1a7bc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1a7bd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	1a7bA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1a7bB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1a7bC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1a7bD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	64.270 Å
Unit-cell length b length_b	80.030 Å
Unit-cell length c length_c	80.470 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	16

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2389
R_work r_work	0.2389
R_free r_free	0.3060

Description description	CD2
Molecular weight formula_weight	10898.3 kDa
Mutation mutation	DEL(M46, K47)
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2956

ENGINEERING A MISFOLDED FORM OF CD2

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

CD2

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 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

fit	/app/data/saxs_computation/a7/1a7b/1a7b.fit
pddf	/app/data/pr_computation/a7/1a7b/1a7b.pr.out
profile	/app/data/saxs_computation/a7/1a7b/1a7b.dat