SAXSdb — 1a64

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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 × 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 4.6；20% MPD, 200MM NACL, 0.1M NACO, PH 4.6	Resolution 2.00 Å R-free 0.273

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 1A64	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 23–121（99 aa） Fragment：DOMAIN 1 Chain B 23–121（99 aa） Fragment：DOMAIN 1 Chain C 23–121（99 aa） Fragment：DOMAIN 1 Chain D 23–121（99 aa） Fragment：DOMAIN 1	Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) Mutation：DEL(M46, K47) Mutation：DEL(M46, K47)	No recorded non-water small molecule	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
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10	Different experimental conditions Different structure-quality metrics	Assembly 2 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 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5	Resolution 3.10 Å R-free 0.306
1A7B ENGINEERING A MISFOLDED FORM OF CD2 Deposited 1998-03-10	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 23–121（99 aa） Fragment：DOMAIN 1 Chain D 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 7.5；2M AMMONIUM SULFATE 2% PEG 400, 0.1M HEPES, PH 7.5	Resolution 3.10 Å R-free 0.306
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 7 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

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	1a64
Deposition date deposition_date	1998-03-05
Structure title title	ENGINEERING A MISFOLDED FORM OF RAT CD2
Keywords keywords	DOMAIN SWAPPING, HINGE LOOP, OLIGOMER EVOLUTION; DOMAIN SWAPPING
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	21.01 Å
Radius of gyration Rg (electron density) rg_electron	20.36 Å
Forward intensity I(0) i0	8024670.00
Molecular weight molecular_weight	21050.0 kDa
Excluded volume excluded_volume	26416 Å³
Envelope volume envelope_volume	32156 Å³
Hydration-shell volume shell_volume	14251 Å³
Envelope diameter envelope_diameter	76.0 Å
Shell Rg shell_rg	25.26 Å
Envelope Rg envelope_rg	20.52 Å
Shape Rg shape_rg	20.34 Å
Total Rg total_rg	21.18 Å
Total atoms total_atoms	1486
Residues n_residues	188
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	80.8 Å
Rg (real space) rg_real	21.16 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	8.0250e+06
I(0) uncertainty (real space) i0_real_error	1.1780e+05
Rg (reciprocal space) rg_reciprocal	21.13 Å
I(0) (reciprocal space) i0_reciprocal	8025000.0000
Solution quality estimate total_estimate	0.7744
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.501
Kurtosis Kurtosis kurtosis	-0.214
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3121000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.532; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.469; Smooth: 1.000

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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	d1a64a_
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	d1a64b_
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 (2 domains)

Domain ID domain_id	1a64A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1a64B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	40.720 Å
Unit-cell length b length_b	40.720 Å
Unit-cell length c length_c	105.840 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2306
R_work r_work	0.2306
R_free r_free	0.2730

Description description	CD2
Molecular weight formula_weight	10898.3 kDa
Mutation mutation	DEL(M46, K47)
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	1549

ENGINEERING A MISFOLDED FORM OF RAT 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 (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	63

fit	/app/data/saxs_computation/a6/1a64/1a64.fit
pddf	/app/data/pr_computation/a6/1a64/1a64.pr.out
profile	/app/data/saxs_computation/a6/1a64/1a64.dat