SAXSdb — 1k5j

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

Nucleoplasmin Core

Xenopus laevis

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–124 Chain B； UniProt 1–124 Chain C； UniProt 1–124 Chain D； UniProt 1–124 Chain E； UniProt 1–124	Fragment：Nucleoplasmin core Mutation：D27N, N61H	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；HEPES, magnesium chloride, PEG-400, 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.252

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 1K5J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EE5 YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A NUCLEOPLASMIN NLS PEPTIDE Deposited 2000-01-30	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 B 152–170（19 aa） Fragment：NLS (NUCLEAR LOCALIZATION SEQUENCE)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.265
1EJY MOUSE IMPORTIN ALPHA-NUCLEOPLASMIN NLS PEPTIDE COMPLEX Deposited 2000-03-05	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 N 155–170（16 aa） Fragment：NLS (NUCLEAR LOCALIZATION SIGNAL) BIPARTITE PEPTIDE, RESIDUES 155-170	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；sodium citrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.268
3UL1 Mouse importin alpha: nucleoplasmin cNLS peptide complex Deposited 2011-11-10	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 A 153–172（20 aa） Fragment：Nucleoplasmin cNLS peptide, residues 153-172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；0.79M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.222

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

View Construct and Data Evidence

UniProt name	NUPL_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； UniProt 1–124 Author chain C； PDBConstruct 1–124； UniProt 1–124 Author chain D； PDBConstruct 1–124； UniProt 1–124 Author chain E； PDBConstruct 1–124； UniProt 1–124

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	1k5j
Deposition date deposition_date	2001-10-10
Structure title title	The Crystal Structure of Nucleoplasmin-Core
Keywords keywords	beta-barrel, jellyroll, beta-bulge, pentamer, CHAPERONE; CHAPERONE
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	22.45 Å
Radius of gyration Rg (electron density) rg_electron	21.08 Å
Forward intensity I(0) i0	36864400.00
Molecular weight molecular_weight	49476.0 kDa
Excluded volume excluded_volume	63089 Å³
Envelope volume envelope_volume	72503 Å³
Hydration-shell volume shell_volume	27322 Å³
Envelope diameter envelope_diameter	67.5 Å
Shell Rg shell_rg	28.99 Å
Envelope Rg envelope_rg	21.32 Å
Shape Rg shape_rg	21.13 Å
Total Rg total_rg	21.89 Å
Total atoms total_atoms	3480
Residues n_residues	462
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	65.0 Å
Rg (real space) rg_real	22.28 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	3.6860e+07
I(0) uncertainty (real space) i0_real_error	4.7200e+05
Rg (reciprocal space) rg_reciprocal	22.32 Å
I(0) (reciprocal space) i0_reciprocal	36870000.0000
Solution quality estimate total_estimate	0.6457
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.5 Å
Skewness Skewness skewness	0.057
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11040000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.977; 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) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1k5ja_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5jb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5jc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5jd_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d1k5je_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

CATH v4.4 (5 domains)

Domain ID domain_id	1k5jA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	1k5jE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

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8. Citations (1)

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Unit-cell length a length_a	116.700 Å
Unit-cell length b length_b	67.100 Å
Unit-cell length c length_c	101.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2510
R_work r_work	0.2189
R_free r_free	0.2516

Description description	Nucleoplasmin Core
Molecular weight formula_weight	13752.7 kDa
Mutation mutation	D27N, N61H
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3627

The Crystal Structure of Nucleoplasmin-Core

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

Nucleoplasmin Core

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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI Class编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

fit	/app/data/saxs_computation/k5/1k5j/1k5j.fit
pddf	/app/data/pr_computation/k5/1k5j/1k5j.pr.out
profile	/app/data/saxs_computation/k5/1k5j/1k5j.dat