SAXSdb — 9x6w

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

LysR family transcriptional regulator

Rhizobium leguminosarum

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 91–310 Chain B； UniProt 91–310 Chain C； UniProt 91–310 Chain D； UniProt 91–310 Chain E； UniProt 91–310 Chain F； UniProt 91–310 Chain G； UniProt 91–310 Chain H； UniProt 91–310	Fragment：NodD-EBD (Effector Binding Domain)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M HEPES pH 7.0, 0.1 M potassium chloride, 15% w/v polyethylene glycol 5,000 MME	Resolution 3.30 Å R-free 0.253

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 9X6W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9IIB Crystal structure of NodD-EBD (Effector Binding Domain) in complex with hesperetin from Rhizobium leguminosarum bv. vicae 3841 Deposited 2024-06-19	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 91–306（216 aa） Chain D 91–306（216 aa）	Not recorded	GOL GLYCEROL × 1 6JP (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.05 M Tris-HCl pH 7.5, 0.2 M potassium chloride, 0.05 M magnesium chloride, 10% w/v polyethylene glycol 4,000	Resolution 2.75 Å R-free 0.252
9IIB Crystal structure of NodD-EBD (Effector Binding Domain) in complex with hesperetin from Rhizobium leguminosarum bv. vicae 3841 Deposited 2024-06-19	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 91–306（216 aa） Chain C 91–306（216 aa）	Not recorded	GOL GLYCEROL × 1 6JP (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.05 M Tris-HCl pH 7.5, 0.2 M potassium chloride, 0.05 M magnesium chloride, 10% w/v polyethylene glycol 4,000	Resolution 2.75 Å R-free 0.252

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

View Construct and Data Evidence

UniProt name	A0A6P0BW74_RHILE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 91–310 Author chain B； PDBConstruct 1–220； UniProt 91–310 Author chain C； PDBConstruct 1–220； UniProt 91–310 Author chain D； PDBConstruct 1–220； UniProt 91–310 Author chain E； PDBConstruct 1–220； UniProt 91–310 Author chain F； PDBConstruct 1–220； UniProt 91–310 Author chain G； PDBConstruct 1–220； UniProt 91–310 Author chain H； PDBConstruct 1–220； UniProt 91–310

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	9x6w
Deposition date deposition_date	2025-10-16
Structure title title	Crystal structure of NodD-EBD (Effector Binding Domain) from Rhizobium leguminosarum bv. vicae 3841
Keywords keywords	NodD, LysR transcription factors, Flavonoids, Rhizobia, TRANSCRIPTION; TRANSCRIPTION
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	39.21 Å
Radius of gyration Rg (electron density) rg_electron	37.98 Å
Forward intensity I(0) i0	468566000.00
Molecular weight molecular_weight	182280.0 kDa
Excluded volume excluded_volume	230940 Å³
Envelope volume envelope_volume	326820 Å³
Hydration-shell volume shell_volume	69176 Å³
Envelope diameter envelope_diameter	116.4 Å
Shell Rg shell_rg	46.65 Å
Envelope Rg envelope_rg	36.51 Å
Shape Rg shape_rg	37.95 Å
Total Rg total_rg	38.65 Å
Total atoms total_atoms	12840
Residues n_residues	1694
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	114.8 Å
Rg (real space) rg_real	38.86 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	4.6860e+08
I(0) uncertainty (real space) i0_real_error	7.7630e+06
Rg (reciprocal space) rg_reciprocal	39.08 Å
I(0) (reciprocal space) i0_reciprocal	468700000.0000
Solution quality estimate total_estimate	0.9009
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.7 Å
Skewness Skewness skewness	0.018
Kurtosis Kurtosis kurtosis	-0.627
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	70640000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.834

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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	192.774 Å
Unit-cell length b length_b	192.774 Å
Unit-cell length c length_c	153.297 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	48.860 Å
R factor r_factor	0.2232
R_work r_work	0.2219
R_free r_free	0.2528

Description description	LysR family transcriptional regulator
Molecular weight formula_weight	25208.4 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	12943

Crystal structure of NodD-EBD (Effector Binding Domain) from Rhizobium leguminosarum bv. vicae 3841

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

LysR family transcriptional regulator

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	Rhizobium leguminosarum
NCBI Class编号 ncbi_taxonomy_id	384
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

fit	/app/data/saxs_computation/x6/9x6w/9x6w.fit
pddf	/app/data/pr_computation/x6/9x6w/9x6w.pr.out
profile	/app/data/saxs_computation/x6/9x6w/9x6w.dat