SAXSdb — 2agj

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

Yvo Fab, Light 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 Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 21–235	Not recorded	Yvo Fab, Heavy Chain × 1 （P01871） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 15000-20000, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.60 Å R-free 0.279

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 2AGJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4YPG Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody Deposited 2015-03-12	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 21–235（215 aa）	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272
4YPG Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody Deposited 2015-03-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 21–235（215 aa）	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.01 M NiCl2, 0.1 M Tris HCl	Resolution 3.00 Å R-free 0.272
6MYY Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs bound, sharpened map Deposited 2018-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01 Chain F 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01 Chain L 127–235（109 aa） Fragment：germline VK3-11 with the mature CDR L3 of VRC01	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6MZJ Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs bound, sharpened map Deposited 2018-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 127–235（109 aa） Fragment：germline VK3-11 with the mature CDRL3 of VRC01 Chain L 127–235（109 aa） Fragment：germline VK3-11 with the mature CDRL3 of VRC01	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6UDK HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074 Deposited 2019-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain E 122–235（114 aa） Chain L 122–235（114 aa） Chain N 122–235（114 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3.5 second blot time, 3 uL sample added to freshly glow-discharged grids	Resolution 3.90 Å
8QH0 Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194 Deposited 2023-09-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 21–234（214 aa）	Not recorded	PRO PROLINE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% PEG 3350, 0.2 M lithium citrate	Resolution 1.87 Å R-free 0.209
8QH1 Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194 Deposited 2023-09-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 21–235（215 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M sodium malonate	Resolution 2.65 Å R-free 0.232

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6PJF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–215； UniProt 21–235

Yvo Fab, Heavy Chain

OrganismNot specified

UniProt P01871

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 Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–183	Non-standard monomer：Yes (specific site not provided by mmCIF)	Yvo Fab, Light Chain × 1 （Q6PJF2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 15000-20000, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.60 Å R-free 0.279

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 2AGJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KXS Cryo-EM structure of human IgM-Fc in complex with the J chain and the ectodomain of pIgR Deposited 2019-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain F 106–453（348 aa） Chain G 106–453（348 aa） Chain H 106–453（348 aa） Chain K 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7K0C Structure of Secretory IgM Core Deposited 2020-09-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 103–453（351 aa） Chain B 103–453（351 aa） Chain E 103–453（351 aa） Chain F 103–453（351 aa） Chain G 103–453（351 aa） Chain H 103–453（351 aa） Chain I 103–453（351 aa） Chain J 103–453（351 aa） Chain K 103–453（351 aa） Chain L 103–453（351 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3.5 seconds before plunging with blot force 7.	Resolution 3.30 Å
7WSP Structure of a membrane protein M Deposited 2022-01-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 106–471（366 aa） Chain D 106–472（367 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.09 Å
7Y09 Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP Deposited 2022-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain F 106–453（348 aa） Chain G 106–453（348 aa） Chain H 106–453（348 aa） Chain K 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
7Y0H Cryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum VAR2CSA FCR3 Deposited 2022-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain F 106–453（348 aa） Chain G 106–453（348 aa） Chain H 106–453（348 aa） Chain K 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
7Y0J Cryo-EM structure of human IgM-Fc in complex with the J chain and the P. falciparum TM284VAR1 Deposited 2022-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain F 106–453（348 aa） Chain G 106–453（348 aa） Chain H 106–453（348 aa） Chain K 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
7YG2 Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP2 Deposited 2022-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain F 106–453（348 aa） Chain G 106–453（348 aa） Chain H 106–453（348 aa） Chain K 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
7YSG Cryo-EM structure of human FcmR bound to sIgM Deposited 2022-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 222–453（232 aa） Chain B 222–453（232 aa） Chain C 222–453（232 aa） Chain D 222–453（232 aa） Chain E 222–453（232 aa） Chain F 222–453（232 aa） Chain G 222–453（232 aa） Chain H 222–453（232 aa） Chain K 222–453（232 aa） Chain L 222–453（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
7YTC Cryo-EM structure of human FcmR bound to IgM-Fc/J Deposited 2022-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 222–453（232 aa） Chain B 222–453（232 aa） Chain C 222–453（232 aa） Chain D 222–453（232 aa） Chain E 222–453（232 aa） Chain F 222–453（232 aa） Chain G 222–453（232 aa） Chain H 222–453（232 aa） Chain K 222–453（232 aa） Chain L 222–453（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
7YTD Cryo-EM structure of four human FcmR bound to IgM-Fc/J Deposited 2022-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 222–452（231 aa） Chain B 222–452（231 aa） Chain C 222–452（231 aa） Chain D 222–452（231 aa） Chain E 222–452（231 aa） Chain F 222–452（231 aa） Chain G 222–452（231 aa） Chain H 222–452（231 aa） Chain K 222–452（231 aa） Chain L 222–452（231 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
8GZN IgM-var2CSA complex Deposited 2022-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain A 1–453（453 aa） Chain B 1–453（453 aa） Chain C 1–453（453 aa） Chain D 1–453（453 aa） Chain E 1–453（453 aa） Chain F 1–453（453 aa） Chain G 1–453（453 aa） Chain H 1–453（453 aa） Chain K 1–453（453 aa） Chain L 1–453（453 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8WYR Cryo-EM structure of human CD5L bound to IgM-Fc/J Deposited 2023-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain F 106–453（348 aa） Chain G 106–453（348 aa） Chain H 106–453（348 aa） Chain K 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
8WYS Local map of human CD5L bound to IgM-Fc/J Deposited 2023-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 106–453（348 aa） Chain L 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
9ARV CryoEM structure of AMETA-A3 Deposited 2024-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 106–453（348 aa） Chain B 106–453（348 aa） Chain C 106–453（348 aa） Chain D 106–453（348 aa） Chain E 106–453（348 aa） Chain L 106–453（348 aa） Chain M 106–453（348 aa） Chain N 106–453（348 aa） Chain O 106–453（348 aa） Chain P 106–453（348 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9UO3 Cryo-EM structure of the human IgM-Fc hexamer Deposited 2025-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 106–446（341 aa） Chain B 106–446（341 aa） Chain C 106–446（341 aa） Chain D 106–446（341 aa） Chain E 106–446（341 aa） Chain F 106–446（341 aa） Chain G 106–446（341 aa） Chain H 106–446（341 aa） Chain I 106–446（341 aa） Chain J 106–446（341 aa） Chain K 106–446（341 aa） Chain L 106–446（341 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9UO4 Cryo-EM structure of the chimeric human IgM-Fc hexamer Deposited 2025-04-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 106–433（328 aa） Chain B 106–433（328 aa） Chain C 106–433（328 aa） Chain D 106–433（328 aa） Chain E 106–433（328 aa） Chain F 106–433（328 aa） Chain G 106–433（328 aa） Chain H 106–433（328 aa） Chain I 106–433（328 aa） Chain J 106–433（328 aa） Chain K 106–433（328 aa） Chain L 106–433（328 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGHM_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 5–224； UniProt 1–183

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	2agj
Deposition date deposition_date	2005-07-27
Structure title title	Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody
Keywords keywords	Antibody, Immunoglobulin superfamily, catalytic antibody, 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	25.84 Å
Radius of gyration Rg (electron density) rg_electron	24.90 Å
Forward intensity I(0) i0	39397900.00
Molecular weight molecular_weight	48289.0 kDa
Excluded volume excluded_volume	60310 Å³
Envelope volume envelope_volume	74053 Å³
Hydration-shell volume shell_volume	24977 Å³
Envelope diameter envelope_diameter	82.2 Å
Shell Rg shell_rg	32.04 Å
Envelope Rg envelope_rg	24.58 Å
Shape Rg shape_rg	24.87 Å
Total Rg total_rg	25.81 Å
Total atoms total_atoms	3400
Residues n_residues	440
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	79.4 Å
Rg (real space) rg_real	25.82 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	3.9400e+07
I(0) uncertainty (real space) i0_real_error	5.7310e+05
Rg (reciprocal space) rg_reciprocal	25.83 Å
I(0) (reciprocal space) i0_reciprocal	39400000.0000
Solution quality estimate total_estimate	0.9049
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.6 Å
Skewness Skewness skewness	0.262
Kurtosis Kurtosis kurtosis	-0.573
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8712000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.852

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Yvo Fab, Light Chain
Molecular weight formula_weight	23367.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3420

EIVLTQSPGTLSLSPGERATLSCRASETVSNDKVAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLSISGLEPEDFVVYYCQQYASSPRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Entity 2 Entity 2 polymer

Description description	Yvo Fab, Heavy Chain
Molecular weight formula_weight	24557.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVTLKESGPTLVKPTQTLTLTCTFSGFSLTTTGEGVGWIRQPPGKALEFLAFIYWNDAKRYNPSLQSRLTITKDASKKQVVLTLTNLDPVDTATYYCARTSGWDIEFEYWGQGTLVTVSSGSASAPTLFPLVSCENSSPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVMQGTDEHVVCKVQHPNGNKEKDVPLPVVI

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2agjh1
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	d2agjh2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2agjl1
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	d2agjl2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	2agjH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2agjH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2agjL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2agjL02
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 (3)

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Unit-cell length a length_a	82.433 Å
Unit-cell length b length_b	103.653 Å
Unit-cell length c length_c	138.715 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	42.200 Å
R factor r_factor	0.2250
R_work r_work	0.2190
R_free r_free	0.2790

fit	/app/data/saxs_computation/ag/2agj/2agj.fit
pddf	/app/data/pr_computation/ag/2agj/2agj.pr.out
profile	/app/data/saxs_computation/ag/2agj/2agj.dat

Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody

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

Yvo Fab, Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Yvo Fab, 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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)