SAXSdb — 1sqw

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

Saccharomyces cerevisiae Nip7p homolog

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–180	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；28% PEG 4000, 0.2M MgCl2, 0.1M sodium acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.261

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 1SQW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1T5Y Crystal Structure of Northeast Structural Genomics Consortium Target HR2118: A Human Homolog of Saccharomyces cerevisiae Nip7p Deposited 2004-05-05	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–180（180 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 5.8；200 mM magnesium sulfate, 20% PEG, 100 mM sodium acetate, 10 mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.294
8FKT Human nucleolar pre-60S ribosomal subunit (State C1) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain NH 1–180（180 aa）	Not recorded	MG MAGNESIUM ION × 64 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.81 Å
8FKU Human nucleolar pre-60S ribosomal subunit (State C2) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain NH 1–180（180 aa）	Not recorded	MG MAGNESIUM ION × 58 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.82 Å
8FKV Human nucleolar pre-60S ribosomal subunit (State D1) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric	Chain NH 1–180（180 aa）	Not recorded	MG MAGNESIUM ION × 65 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.47 Å
8FKW Human nucleolar pre-60S ribosomal subunit (State D2) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain NH 1–180（180 aa）	Not recorded	MG MAGNESIUM ION × 59 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.50 Å
8FKX Human nucleolar pre-60S ribosomal subunit (State E) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain NH 1–180（180 aa）	Not recorded	MG MAGNESIUM ION × 61 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.59 Å
8FKY Human nucleolar pre-60S ribosomal subunit (State F) Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 59-meric	Chain NH 1–180（180 aa）	Not recorded	MG MAGNESIUM ION × 70 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.	Resolution 2.67 Å

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

View Construct and Data Evidence

UniProt name	NIP7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 1–180

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	1sqw
Deposition date deposition_date	2004-03-19
Structure title title	Crystal structure of KD93, a novel protein expressed in the human pro
Keywords keywords	PUA, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	18.58 Å
Radius of gyration Rg (electron density) rg_electron	17.56 Å
Forward intensity I(0) i0	7158500.00
Molecular weight molecular_weight	20005.0 kDa
Excluded volume excluded_volume	25284 Å³
Envelope volume envelope_volume	29350 Å³
Hydration-shell volume shell_volume	14669 Å³
Envelope diameter envelope_diameter	66.5 Å
Shell Rg shell_rg	22.70 Å
Envelope Rg envelope_rg	17.86 Å
Shape Rg shape_rg	17.48 Å
Total Rg total_rg	18.68 Å
Total atoms total_atoms	1409
Residues n_residues	176
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	67.6 Å
Rg (real space) rg_real	18.58 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	7.1590e+06
I(0) uncertainty (real space) i0_real_error	8.9560e+04
Rg (reciprocal space) rg_reciprocal	18.58 Å
I(0) (reciprocal space) i0_reciprocal	7158000.0000
Solution quality estimate total_estimate	0.8444
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.4 Å
Skewness Skewness skewness	0.361
Kurtosis Kurtosis kurtosis	-0.203
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1467000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 0.992

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1sqwa1
Class class	b — All beta proteins
Fold Fold fold	b.122 — PUA domain-like
Superfamily Superfamily superfamily	b.122.1 — PUA domain-like
Family Family family	b.122.1.1 — PUA domain

Domain ID domain_id	d1sqwa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.6 — Pre-PUA domain
Family Family family	d.17.6.3 — Nip7p homolog, N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1sqwA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	1sqwA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily	10 — PUA domain

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8. Citations (1)

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Unit-cell length a length_a	57.203 Å
Unit-cell length b length_b	57.203 Å
Unit-cell length c length_c	132.048 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	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.2250
R_free r_free	0.2610

Description description	Saccharomyces cerevisiae Nip7p homolog
Molecular weight formula_weight	21562.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1540

Crystal structure of KD93, a novel protein expressed in the human pro

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

Saccharomyces cerevisiae Nip7p homolog

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
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	131

fit	/app/data/saxs_computation/sq/1sqw/1sqw.fit
pddf	/app/data/pr_computation/sq/1sqw/1sqw.pr.out
profile	/app/data/saxs_computation/sq/1sqw/1sqw.dat