SAXSdb — 4cbp

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

NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2

DROSOPHILA MELANOGASTER

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 5–267 Chain B； UniProt 5–267	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；HANGING-DROP EXPERIMENTS BY MIXING 1 UL PROTEIN (5.5. MG/ML IN 10 MM HEPES PH 7.4, 20 MM NACL) AND 1 UL RESERVOIR SOLUTION (17% PEG-6000, 0.1 M TRIS HYDROCHLORIDE, PH 7.0)	Resolution 1.60 Å R-free 0.188

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 4CBP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6FEY Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin Deposited 2018-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 26–267（242 aa） Chain B 26–267（242 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5	Resolution 3.48 Å R-free 0.345
6FEY Crystal structure of Drosophila neural ectodermal development factor Imp-L2 with Drosophila DILP5 insulin Deposited 2018-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 26–267（242 aa） Chain D 26–267（242 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；Cp 10 mg/ml, 8-10% w/v PEG 4k or 6K, 20 mM MgCl2, 0.1 M HEPES pH 6.8-7.5	Resolution 3.48 Å R-free 0.345
6FF3 Crystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I Deposited 2018-01-03	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 A 26–267（242 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；cp 10 mg/ml, 4-8% w/v PEG 6K, 5-20 mM MgCl2, 5 mM SB12, 0.1 M TRIS pH 7.5	Resolution 2.57 Å R-free 0.285

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IMPL2_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 5–267 Author chain B； PDBConstruct 1–263； UniProt 5–267

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	4cbp
Deposition date deposition_date	2013-10-15
Structure title title	Crystal structure of neural ectodermal development factor IMP-L2.
Keywords keywords	CELL ADHESION, IMAGINAL MORPHOGENESIS PROTEIN-LATE 2, INSULIN BINDING, IMMUNOGLOBULIN DOMAIN, DEVELOPMENTAL PROTEIN; CELL ADHESION
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	23.69 Å
Radius of gyration Rg (electron density) rg_electron	22.54 Å
Forward intensity I(0) i0	39590500.00
Molecular weight molecular_weight	47074.0 kDa
Excluded volume excluded_volume	58384 Å³
Envelope volume envelope_volume	72843 Å³
Hydration-shell volume shell_volume	26430 Å³
Envelope diameter envelope_diameter	80.0 Å
Shell Rg shell_rg	30.14 Å
Envelope Rg envelope_rg	22.84 Å
Shape Rg shape_rg	22.59 Å
Total Rg total_rg	23.34 Å
Total atoms total_atoms	3282
Residues n_residues	405
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	76.7 Å
Rg (real space) rg_real	23.55 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	3.9590e+07
I(0) uncertainty (real space) i0_real_error	4.9660e+05
Rg (reciprocal space) rg_reciprocal	23.58 Å
I(0) (reciprocal space) i0_reciprocal	39590000.0000
Solution quality estimate total_estimate	0.6966
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6174000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

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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	NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2
Molecular weight formula_weight	30325.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3869

MNLHVCALALLLFGSIATVRGRAVDLVDDSNDVDNSIEAEEEKPRNRAFEADWLKFTKTPPTKLQQADGATIEIVCEMMGSQVPSIQWVVGHLPRSELDDLDSNQVAEEAPSAIVRVRSSHIIDHVLSEARTYTCVGRTGSKTIYASTVVHPPRSSRLTPEKTYPGAQKPRIIYTEKTHLDLMGSNIQLPCRVHARPRAEITWLNNENKEIVQGHRHRVLANGDLLISEIKWEDMGNYKCIARNVVGKDTADTFVYPVLNEEDEVLFQ

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
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	457

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4cbpA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4cbpA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4cbpB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4cbpB02
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	49.856 Å
Unit-cell length b length_b	99.732 Å
Unit-cell length c length_c	56.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	29.542 Å
R factor r_factor	0.1571
R_work r_work	0.1562
R_free r_free	0.1883

fit	/app/data/saxs_computation/cb/4cbp/4cbp.fit
pddf	/app/data/pr_computation/cb/4cbp/4cbp.pr.out
profile	/app/data/saxs_computation/cb/4cbp/4cbp.dat

Crystal structure of neural ectodermal development factor IMP-L2.

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

NEURAL/ECTODERMAL DEVELOPMENT FACTOR IMP-L2

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