SAXSdb — 6ekb

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

DnaJ/Hsp40 cysteine-rich domain superfamily protein

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 57–136	Mutation：K56M	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20 % PEG 10,000, 8 % ethylene glycol and 0.1 M HEPES-NaOH pH 7.5	Resolution 1.90 Å R-free 0.216

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 6EKB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain B8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain T1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain T8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain D8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain F1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain F8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain H1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain H8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain J1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain J8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain L1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain L8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain N1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain N8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain P1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain P8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain R1 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R2 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R3 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R4 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R5 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R6 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R7 57–136（80 aa） Fragment：mature protein, residues 53-136 Chain R8 57–136（80 aa） Fragment：mature protein, residues 53-136	Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
8ILB The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) Deposited 2023-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain F 57–136（80 aa） Chain G 57–136（80 aa） Chain H 57–136（80 aa） Chain I 57–136（80 aa） Chain O 57–136（80 aa） Chain P 57–136（80 aa） Chain Q 57–136（80 aa） Chain R 57–136（80 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain C 57–136（80 aa） Chain L 57–136（80 aa） Chain M 57–136（80 aa） Chain N 57–136（80 aa） Chain O 57–136（80 aa） Chain P 57–136（80 aa） Chain Q 57–136（80 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
9CI2 Anthoceros agrestis Rubisco octamer core complexed with small subunits and Arabidopsis thaliana BSD2 Deposited 2024-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain 1 1–136（136 aa） Chain 2 1–136（136 aa） Chain 3 1–136（136 aa） Chain 4 1–136（136 aa）	Not recorded	MG MAGNESIUM ION × 4 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris pH 8.0 50 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

4 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9SN73_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–81； UniProt 57–136

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	6ekb
Deposition date deposition_date	2017-09-26
Structure title title	Crystal structure of the BSD2 homolog of Arabidopsis thaliana
Keywords keywords	zinc finger, assembly chaperone, Rubisco, 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	13.98 Å
Radius of gyration Rg (electron density) rg_electron	13.92 Å
Forward intensity I(0) i0	1169000.00
Molecular weight molecular_weight	6463.0 kDa
Excluded volume excluded_volume	7677 Å³
Envelope volume envelope_volume	9395 Å³
Hydration-shell volume shell_volume	6640 Å³
Envelope diameter envelope_diameter	52.0 Å
Shell Rg shell_rg	17.43 Å
Envelope Rg envelope_rg	14.43 Å
Shape Rg shape_rg	14.08 Å
Total Rg total_rg	14.33 Å
Total atoms total_atoms	435
Residues n_residues	62
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	56.9 Å
Rg (real space) rg_real	14.21 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.1690e+06
I(0) uncertainty (real space) i0_real_error	1.5850e+04
Rg (reciprocal space) rg_reciprocal	14.20 Å
I(0) (reciprocal space) i0_reciprocal	1169000.0000
Solution quality estimate total_estimate	0.6459
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.2 Å
Skewness Skewness skewness	0.588
Kurtosis Kurtosis kurtosis	-0.165
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	80750.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.436; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.084; Smooth: 0.000

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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	DnaJ/Hsp40 cysteine-rich domain superfamily protein
Molecular weight formula_weight	8355.5 kDa
Mutation mutation	K56M
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	464

MAANNNPQGTKPNSLVCANCEGEGCVACSQCKGGGVNLIDHFNGQFKAGALCWLCRGKKEVLCGDCNGAGFIGGFLSTFDE

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	29

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8. Citations (1)

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Unit-cell length a length_a	55.708 Å
Unit-cell length b length_b	55.708 Å
Unit-cell length c length_c	48.131 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	30.000 Å
R factor r_factor	0.1901
R_work r_work	0.1888
R_free r_free	0.2158

fit	/app/data/saxs_computation/ek/6ekb/6ekb.fit
pddf	/app/data/pr_computation/ek/6ekb/6ekb.pr.out
profile	/app/data/saxs_computation/ek/6ekb/6ekb.dat

Crystal structure of the BSD2 homolog of Arabidopsis thaliana

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

DnaJ/Hsp40 cysteine-rich domain superfamily protein

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