SAXSdb — 1dcl

▼

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

MCG

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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 21–235 Chain B； UniProt 21–235	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：CRYSTALLIZED FROM AMMONIUM SULFATE	Resolution 2.30 Å

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 1DCL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A8J IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG) COMPLEX WITH ASPARTAME Deposited 1998-03-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 21–235（215 aa） Chain L 21–235（215 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PME N-L-ALPHA-ASPARTYL L-PHENYLALANINE 1-METHYL ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；PROTEIN WAS CRYSTALLIZED IN FRESH 1.9M AMMONIUM SULFATE BUFFERED AT PH 6.2 WITH PHOSPHATE AND THE MOTHER LIQUOR WAS SATURATED WITH ASPARTAME.	Resolution 2.70 Å R-free 0.380
2MCG THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS Deposited 1989-05-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 21–235（215 aa） Chain 2 21–235（215 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
4UNT Induced monomer of the Mcg variable domain Deposited 2014-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain B 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain C 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain D 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain E 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain F 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain G 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain H 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	SO4 SULFATE ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.5M LICL, 1.65M (NH4)2SO4, pH 8	Resolution 2.70 Å R-free 0.289
4UNU MCG - a dimer of lambda variable domains Deposited 2014-05-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain B 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110	Not recorded	15P POLYETHYLENE GLYCOL (N=34) × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；2M NACL, 2M (NH4)2SO4, pH 8	Resolution 0.95 Å R-free 0.130
4UNV Covalent dimer of lambda variable domains Deposited 2014-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110	Mutation：YES	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M CH3COONA PH4.6, 2M (NH4)2SO4	Resolution 1.60 Å R-free 0.258
5ACL Mcg immunoglobulin variable domain with sulfasalazine Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa） Fragment：IG LAMBDA CHAIN V-II REGION MGC	Not recorded	SAS 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2 M TRI-POTASSIUM CITRATE, 2.2 M (NH4)2SO4, 0.5 M SULFASALAZINE, pH 8.5	Resolution 1.49 Å R-free 0.187
5ACM Mcg immunoglobulin variable domain with methylene blue Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa） Fragment：IG LAMBDA CHAIN V-II REGION MGC	Not recorded	MBT 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5	Resolution 1.05 Å R-free 0.122
5ACM Mcg immunoglobulin variable domain with methylene blue Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–110（110 aa） Fragment：IG LAMBDA CHAIN V-II REGION MGC	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5	Resolution 1.05 Å R-free 0.122

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

View Construct and Data Evidence

UniProt name	LV2F_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–216； UniProt 21–235 Author chain B； PDBConstruct 2–216； UniProt 21–235

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	1dcl
Deposition date deposition_date	1995-10-16
Structure title title	MCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRYSTALLIZED FROM AMMONIUM SULFATE
Keywords keywords	IMMUNOGLOBULIN, BENCE JONES, ANTIBODY, MULTIPLE QUATERNARY STRUCTURES; IMMUNOGLOBULIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.70 Å
Radius of gyration Rg (electron density) rg_electron	23.66 Å
Forward intensity I(0) i0	36752900.00
Molecular weight molecular_weight	45562.0 kDa
Excluded volume excluded_volume	56425 Å³
Envelope volume envelope_volume	69040 Å³
Hydration-shell volume shell_volume	24599 Å³
Envelope diameter envelope_diameter	79.3 Å
Shell Rg shell_rg	30.56 Å
Envelope Rg envelope_rg	23.47 Å
Shape Rg shape_rg	23.64 Å
Total Rg total_rg	24.51 Å
Total atoms total_atoms	3208
Residues n_residues	432
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	79.0 Å
Rg (real space) rg_real	24.67 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.6750e+07
I(0) uncertainty (real space) i0_real_error	5.7310e+05
Rg (reciprocal space) rg_reciprocal	24.68 Å
I(0) (reciprocal space) i0_reciprocal	36750000.0000
Solution quality estimate total_estimate	0.9022
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.421
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4757000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.949

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dcla1
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	d1dcla2
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	d1dclb1
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	d1dclb2
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	1dclA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dclA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dclB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1dclB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (3)

▶

Unit-cell length a length_a	72.300 Å
Unit-cell length b length_b	72.300 Å
Unit-cell length c length_c	185.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	0.1400
R_free r_free	—

Description description	MCG
Molecular weight formula_weight	22818.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3621

MCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRYSTALLIZED FROM AMMONIUM SULFATE

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

MCG

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 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)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	413

fit	/app/data/saxs_computation/dc/1dcl/1dcl.fit
pddf	/app/data/pr_computation/dc/1dcl/1dcl.pr.out
profile	/app/data/saxs_computation/dc/1dcl/1dcl.dat