SAXSdb — 5day

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

NAP1-related protein 1

Arabidopsis thaliana

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 19–225 Chain B； UniProt 19–225	Fragment：UNP RESIDUES 19-225	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；289.15 K；25% PEG 400, 0.1 M HEPES pH 7.6, 0.2 M Calcium chloride dihydrate	Resolution 2.33 Å R-free 0.269

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 5DAY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7BP6 Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-03-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 226–232（7 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；0.2 M sodium nitrate, 0.1 M Bis-Tris propane and 20% (w/v) PEG 3350 (pH 8.5)	Resolution 1.58 Å R-free 0.200
7C7X Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1) Deposited 2020-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 19–256（238 aa） Chain F 19–256（238 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol	Resolution 3.00 Å R-free 0.262

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

View Construct and Data Evidence

UniProt name	NRP1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–208； UniProt 19–225 Author chain B； PDBConstruct 2–208； UniProt 19–225

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	5day
Deposition date deposition_date	2015-08-20
Structure title title	The structure of NAP1-Related Protein(NRP1) in Arabidopsis
Keywords keywords	histone chaperone, NAP1-Related protein, transcriptional activation, 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	27.33 Å
Radius of gyration Rg (electron density) rg_electron	26.93 Å
Forward intensity I(0) i0	24911700.00
Molecular weight molecular_weight	40188.0 kDa
Excluded volume excluded_volume	50937 Å³
Envelope volume envelope_volume	67840 Å³
Hydration-shell volume shell_volume	22409 Å³
Envelope diameter envelope_diameter	100.0 Å
Shell Rg shell_rg	32.60 Å
Envelope Rg envelope_rg	26.50 Å
Shape Rg shape_rg	26.89 Å
Total Rg total_rg	27.77 Å
Total atoms total_atoms	2844
Residues n_residues	345
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	97.1 Å
Rg (real space) rg_real	27.52 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	2.4910e+07
I(0) uncertainty (real space) i0_real_error	4.4160e+05
Rg (reciprocal space) rg_reciprocal	27.46 Å
I(0) (reciprocal space) i0_reciprocal	24910000.0000
Solution quality estimate total_estimate	0.8499
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.450
Kurtosis Kurtosis kurtosis	-0.350
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3455000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.788; Smooth: 0.996

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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	NAP1-related protein 1
Molecular weight formula_weight	23992.6 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	2945

SNLEQIDAELVLSIEKLQEIQDDLEKINEKASDEVLEVEQKYNVIRKPVYDKRNEVIQSIPGFWMTAFLSHPALGDLLTEEDQKIFKYLNSLEVEDAKDVKSGYSITFHFTSNPFFEDAKLTKTFTFLEEGTTKITATPIKWKEGKGLPNGVNHDDKKGNKRALPEESFFTWFTDAQHKEDAGDEIHDEVADIIKEDLWSNPLTYFNN

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	Mouse-ear cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5daya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.305 — NAP-like
Superfamily Superfamily superfamily	d.305.1 — NAP-like
Family Family family	d.305.1.0 — automated matches

Domain ID domain_id	d5daya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5dayb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.305 — NAP-like
Superfamily Superfamily superfamily	d.305.1 — NAP-like
Family Family family	d.305.1.0 — automated matches

Domain ID domain_id	d5dayb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5dayA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	90 — Nucleosome assembly protein

Domain ID domain_id	5dayB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	90 — Nucleosome assembly protein

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8. Citations (1)

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Unit-cell length a length_a	60.542 Å
Unit-cell length b length_b	60.812 Å
Unit-cell length c length_c	135.248 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.329 Å
Low-resolution limit resolution_low	45.218 Å
R factor r_factor	0.2336
R_work r_work	0.2300
R_free r_free	0.2688

fit	/app/data/saxs_computation/da/5day/5day.fit
pddf	/app/data/pr_computation/da/5day/5day.pr.out
profile	/app/data/saxs_computation/da/5day/5day.dat

The structure of NAP1-Related Protein(NRP1) in Arabidopsis

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

NAP1-related protein 1

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