SAXSdb — 4wt3

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

Rubisco Accumulation Factor 1, isoform 2

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 62–274	Fragment：Raf1 alpha-domain, UNP residues 62-274	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES-NaOH pH 6.0 and 26% (w/v) PEG-6000	Resolution 1.95 Å R-free 0.246

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 4WT3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WT4 The C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form I Deposited 2014-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449 Chain C 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG 3350	Resolution 2.81 Å R-free 0.289
4WT4 The C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form I Deposited 2014-10-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449 Chain D 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG 3350	Resolution 2.81 Å R-free 0.289
4WT5 The C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form II Deposited 2014-10-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric	Chain A 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449 Chain B 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；200 mM KH2PO4 and 20% (w/v) PEG-5000MME	Resolution 2.57 Å R-free 0.279
8ILB The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) Deposited 2023-03-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain E 62–449（388 aa） Chain N 62–449（388 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8ILM The cryo-EM structure of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2) Deposited 2023-03-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain D 62–449（388 aa） Chain E 62–449（388 aa） Chain R 62–449（388 aa） Chain S 62–449（388 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8IO2 The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL) Deposited 2023-03-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain I 73–437（365 aa） Chain J 73–437（365 aa） Chain K 73–437（365 aa） Chain L 73–437（365 aa） Chain M 73–437（365 aa） Chain N 73–437（365 aa） Chain O 73–437（365 aa） Chain P 73–437（365 aa） Chain Q 73–437（365 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8IOJ The Rubisco assembly intermidiate of Rubisco large subunit (RbcL) and Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) Deposited 2023-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain E 62–264（203 aa） Chain F 62–264（203 aa） Chain G 62–264（203 aa） Chain L 287–437（151 aa） Chain M 287–437（151 aa） Chain N 287–437（151 aa） Chain O 287–437（151 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

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

View Construct and Data Evidence

UniProt name	RAF2_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–213； UniProt 62–274

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	4wt3
Deposition date deposition_date	2014-10-29
Structure title title	The N-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana
Keywords keywords	assembly chaperone, 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	21.24 Å
Radius of gyration Rg (electron density) rg_electron	20.70 Å
Forward intensity I(0) i0	8836130.00
Molecular weight molecular_weight	21940.0 kDa
Excluded volume excluded_volume	27404 Å³
Envelope volume envelope_volume	32585 Å³
Hydration-shell volume shell_volume	14633 Å³
Envelope diameter envelope_diameter	76.4 Å
Shell Rg shell_rg	25.24 Å
Envelope Rg envelope_rg	21.08 Å
Shape Rg shape_rg	20.69 Å
Total Rg total_rg	21.40 Å
Total atoms total_atoms	3068
Residues n_residues	198
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	78.2 Å
Rg (real space) rg_real	21.48 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	8.8360e+06
I(0) uncertainty (real space) i0_real_error	1.2300e+05
Rg (reciprocal space) rg_reciprocal	21.44 Å
I(0) (reciprocal space) i0_reciprocal	8836000.0000
Solution quality estimate total_estimate	0.7660
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.563
Kurtosis Kurtosis kurtosis	-0.285
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3375000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.523; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.399; Smooth: 0.986

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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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8. Citations (1)

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Unit-cell length a length_a	29.769 Å
Unit-cell length b length_b	29.769 Å
Unit-cell length c length_c	457.085 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	1.954 Å
Low-resolution limit resolution_low	29.706 Å
R factor r_factor	0.2129
R_work r_work	0.2113
R_free r_free	0.2456

Description description	Rubisco Accumulation Factor 1, isoform 2
Molecular weight formula_weight	24004.9 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	3178

The N-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana

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

Rubisco Accumulation Factor 1, isoform 2

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

fit	/app/data/saxs_computation/wt/4wt3/4wt3.fit
pddf	/app/data/pr_computation/wt/4wt3/4wt3.pr.out
profile	/app/data/saxs_computation/wt/4wt3/4wt3.dat