SAXSdb — 2i6f

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

Response regulator FrzS

Myxococcus xanthus

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 1–124	Fragment：Receiver domain (residues 1-124)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 3350, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.254
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–124	Fragment：Receiver domain (residues 1-124)	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 3350, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.254
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–124	Fragment：Receiver domain (residues 1-124)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 3350, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.254

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 2I6F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–117（115 aa）	Mutation：C318S Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2	Resolution 2.44 Å R-free 0.235
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–117（115 aa）	Mutation：C318S Non-standard monomer：Yes (specific site not provided by mmCIF)	CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2	Resolution 2.44 Å R-free 0.235
9QY8 Crystal structure of apoform human USP18 Deposited 2025-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20 % (w/v) PEG3350	Resolution 1.92 Å R-free 0.260
9QY8 Crystal structure of apoform human USP18 Deposited 2025-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–124（124 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20 % (w/v) PEG3350	Resolution 1.92 Å R-free 0.260

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

View Construct and Data Evidence

UniProt name	Q1D4U9_MYXXD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–127； UniProt 1–124 Author chain B； PDBConstruct 4–127； UniProt 1–124 Author chain C； PDBConstruct 4–127； UniProt 1–124

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	2i6f
Deposition date deposition_date	2006-08-28
Structure title title	Receiver domain from Myxococcus xanthus social motility protein FrzS
Keywords keywords	Social motility, signaling, receiver domain, two-component, SIGNALING PROTEIN; SIGNALING PROTEIN
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	24.34 Å
Radius of gyration Rg (electron density) rg_electron	23.30 Å
Forward intensity I(0) i0	25306400.00
Molecular weight molecular_weight	37984.0 kDa
Excluded volume excluded_volume	47448 Å³
Envelope volume envelope_volume	58543 Å³
Hydration-shell volume shell_volume	21654 Å³
Envelope diameter envelope_diameter	76.5 Å
Shell Rg shell_rg	29.20 Å
Envelope Rg envelope_rg	23.03 Å
Shape Rg shape_rg	23.30 Å
Total Rg total_rg	24.05 Å
Total atoms total_atoms	2670
Residues n_residues	363
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	74.8 Å
Rg (real space) rg_real	24.31 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.5310e+07
I(0) uncertainty (real space) i0_real_error	3.3210e+05
Rg (reciprocal space) rg_reciprocal	24.32 Å
I(0) (reciprocal space) i0_reciprocal	25310000.0000
Solution quality estimate total_estimate	0.9091
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.225
Kurtosis Kurtosis kurtosis	-0.642
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7744000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.969

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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	Response regulator FrzS
Molecular weight formula_weight	13686.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2957

GSHMSKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVIIGNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALIGFPE

来源 Source

来源生物 organism	Myxococcus xanthus
NCBI Class编号 ncbi_taxonomy_id	34
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2i6fa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.0 — automated matches

Domain ID domain_id	d2i6fb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.0 — automated matches

Domain ID domain_id	d2i6fc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2i6fA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2i6fB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	2i6fC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (1)

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Unit-cell length a length_a	142.479 Å
Unit-cell length b length_b	142.479 Å
Unit-cell length c length_c	37.420 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	24

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2217
R_work r_work	0.2199
R_free r_free	0.2537

fit	/app/data/saxs_computation/i6/2i6f/2i6f.fit
pddf	/app/data/pr_computation/i6/2i6f/2i6f.pr.out
profile	/app/data/saxs_computation/i6/2i6f/2i6f.dat

Receiver domain from Myxococcus xanthus social motility protein FrzS

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

Response regulator FrzS

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