SAXSdb — 4ndk

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

E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,

Eimeria acervulina

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 1–239 Chain B； UniProt 1–239	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium chloride, 12% v/v 2-propanol, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247

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 4NDK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NDJ Crystal Structure of a computational designed engrailed homeodomain variant fused with YFP Deposited 2013-10-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–239（239 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.8 M monosodium phosphate, 1.2 M dipotassium phosphate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.200
6RMG Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II Deposited 2019-05-06	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 × 2 PDB declaration: dimeric	Chain A 2–241（240 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 11 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9P0K Composite map of CXCL9-CXCR3-Gi-scFv16 Deposited 2025-06-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9P0L Composite map of CXCL10-CXCR3-Gi-scFv16 Deposited 2025-06-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9P0M Composite map of CXCL11-CXCR3-Gi-scFv16 Deposited 2025-06-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–239（239 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	U6GSR1_EIMAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 53–289； UniProt 1–239 Author chain B； PDBConstruct 53–289； UniProt 1–239

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	4ndk
Deposition date deposition_date	2013-10-26
Structure title title	Crystal structure of a computational designed engrailed homeodomain variant fused with YFP
Keywords keywords	helix-turn-helix, fluorescent protein, de novo protein; fluorescent protein, de novo protein
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	32.37 Å
Radius of gyration Rg (electron density) rg_electron	32.26 Å
Forward intensity I(0) i0	61657500.00
Molecular weight molecular_weight	63005.0 kDa
Excluded volume excluded_volume	78985 Å³
Envelope volume envelope_volume	99120 Å³
Hydration-shell volume shell_volume	27040 Å³
Envelope diameter envelope_diameter	118.1 Å
Shell Rg shell_rg	37.30 Å
Envelope Rg envelope_rg	32.19 Å
Shape Rg shape_rg	32.25 Å
Total Rg total_rg	32.68 Å
Total atoms total_atoms	4454
Residues n_residues	543
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	108.9 Å
Rg (real space) rg_real	32.79 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	6.1660e+07
I(0) uncertainty (real space) i0_real_error	9.5860e+05
Rg (reciprocal space) rg_reciprocal	32.62 Å
I(0) (reciprocal space) i0_reciprocal	61650000.0000
Solution quality estimate total_estimate	0.7286
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.501
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16970000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.630; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.582; Smooth: 0.000

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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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4ndkA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

Domain ID domain_id	4ndkB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	155 — Green Fluorescent Protein
Homologous superfamily homologous superfamily	10 — Green fluorescent protein

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8. Citations (1)

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Unit-cell length a length_a	75.890 Å
Unit-cell length b length_b	192.650 Å
Unit-cell length c length_c	107.610 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	34.000 Å
R factor r_factor	0.1929
R_work r_work	0.1901
R_free r_free	0.2473

Description description	E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,
Molecular weight formula_weight	34510.9 kDa
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	4852

Crystal structure of a computational designed engrailed homeodomain variant fused with YFP

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

E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,

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) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Eimeria acervulina
通用名 common_name	Coccidian parasite
NCBI Class编号 ncbi_taxonomy_id	5801
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	398

fit	/app/data/saxs_computation/nd/4ndk/4ndk.fit
pddf	/app/data/pr_computation/nd/4ndk/4ndk.pr.out
profile	/app/data/saxs_computation/nd/4ndk/4ndk.dat