SAXSdb — 2rgs

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

Ig gamma-2B heavy chain

OrganismNot specified

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 Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 117–334 Chain B； UniProt 117–334	Fragment：Fc-fragment	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；301 K；20% PEG2000, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K	Resolution 2.13 Å R-free 0.213

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 2RGS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CIC IDIOTOPE-ANTI-IDIOTOPE FAB-FAB COMPLEX; D1.3-E225 Deposited 1999-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–217（217 aa） Fragment：FAB IMMUNOGLOBULIN FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；12% PEG 800, 75 MILLIMOLAR SODIUM ACETATE PH 4.85 10MGM/ML PROTEIN CONCENTRATION , pH 4.9	Resolution 2.50 Å
1HQ4 STRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4 Deposited 2000-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–99（99 aa） Fragment：VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.265
1HQ4 STRUCTURE OF NATIVE CATALYTIC ANTIBODY HA5-19A4 Deposited 2000-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–99（99 aa） Fragment：VARIABLE REGIONS OF FAB LIGHT AND HEAVY CHAINS	Not recorded	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；PEG 6000, cadmium chloride, hepes, ph 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.265
1MAM CRYSTAL STRUCTURE TO 2.45 A RESOLUTION OF A MONOCLONAL FAB SPECIFIC FOR THE BRUCELLA A CELL WALL POLYSACCHARIDE ANTIGEN Deposited 1992-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å
1NBV AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX Deposited 1993-03-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1OSP CRYSTAL STRUCTURE OF OUTER SURFACE PROTEIN A OF BORRELIA BURGDORFERI COMPLEXED WITH A MURINE MONOCLONAL ANTIBODY FAB Deposited 1996-11-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–98（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å R-free 0.295
5UBX Crystal structure of a mutant mIgG2b Fc heterodimer in complex with Protein A peptide analog Z34C Deposited 2016-12-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 108–335（228 aa） Fragment：UNP residues 108-335 Chain B 108–335（228 aa） Fragment：UNP residues 108-335	Mutation：P307T, Q309L, V370K, K409R Mutation：I253D, F405L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；17% PEG 3350, 0.2 M LiCl, 0.1 M Tris, pH 8.0	Resolution 2.70 Å R-free 0.257
6KRU Crystal structure of mouse IgG2b Fc Deposited 2019-08-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–334（218 aa） Chain B 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.237
6KRU Crystal structure of mouse IgG2b Fc Deposited 2019-08-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 117–334（218 aa） Chain D 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.237
6KRU Crystal structure of mouse IgG2b Fc Deposited 2019-08-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 117–334（218 aa） Chain F 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；16% PEG3350, 0.2 M lithium chloride, and 0.1 M Bis-Tris (pH 6.5)	Resolution 2.30 Å R-free 0.237
6KRV Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A Deposited 2019-08-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 117–334（218 aa） Chain B 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% (v/v) Tacsimate (pH 7.0)	Resolution 3.30 Å R-free 0.250
6KRV Crystal structure of mouse IgG2b Fc complexed with B domain of Protein A Deposited 2019-08-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 117–334（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；60% (v/v) Tacsimate (pH 7.0)	Resolution 3.30 Å R-free 0.250

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCBM_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–218； UniProt 117–334 Author chain B； PDBConstruct 1–218； UniProt 117–334

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	2rgs
Deposition date deposition_date	2007-10-05
Structure title title	FC-fragment of monoclonal antibody IGG2B from Mus musculus
Keywords keywords	Fc-fragment, immunoglobulin, glycosylation, IMMUNE SYSTEM; IMMUNE SYSTEM
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	25.74 Å
Radius of gyration Rg (electron density) rg_electron	24.50 Å
Forward intensity I(0) i0	41377300.00
Molecular weight molecular_weight	49997.0 kDa
Excluded volume excluded_volume	62729 Å³
Envelope volume envelope_volume	80581 Å³
Hydration-shell volume shell_volume	27196 Å³
Envelope diameter envelope_diameter	78.0 Å
Shell Rg shell_rg	31.94 Å
Envelope Rg envelope_rg	24.01 Å
Shape Rg shape_rg	24.50 Å
Total Rg total_rg	25.38 Å
Total atoms total_atoms	3513
Residues n_residues	413
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	75.4 Å
Rg (real space) rg_real	25.58 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	4.1380e+07
I(0) uncertainty (real space) i0_real_error	5.1950e+05
Rg (reciprocal space) rg_reciprocal	25.63 Å
I(0) (reciprocal space) i0_reciprocal	41380000.0000
Solution quality estimate total_estimate	0.9169
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.3 Å
Skewness Skewness skewness	0.026
Kurtosis Kurtosis kurtosis	-0.609
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5647000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ig gamma-2B heavy chain
Molecular weight formula_weight	24530.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4127

CPAPNLEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMKTSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPG

Entity 2 Entity 2 branched

Description description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1625.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	533

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2rgsa1
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.1.1.0 — automated matches

Domain ID domain_id	d2rgsa2
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.1.1.0 — automated matches

Domain ID domain_id	d2rgsb1
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.1.1.0 — automated matches

Domain ID domain_id	d2rgsb2
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.1.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2rgsA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2rgsA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2rgsB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2rgsB02
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	138.946 Å
Unit-cell length b length_b	63.956 Å
Unit-cell length c length_c	72.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2015
R_work r_work	0.2006
R_free r_free	0.2130

fit	/app/data/saxs_computation/rg/2rgs/2rgs.fit
pddf	/app/data/pr_computation/rg/2rgs/2rgs.pr.out
profile	/app/data/saxs_computation/rg/2rgs/2rgs.dat

FC-fragment of monoclonal antibody IGG2B from Mus musculus

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

Ig gamma-2B heavy chain

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