SAXSdb — 1x3u

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

Transcriptional regulatory protein fixJ

Sinorhizobium meliloti

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 130–204	Fragment：C-TERMINAL DOMAIN	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.5；298 K；Pressure 1 NMR sample composition：1mM FixJC U-15N,13C; 20mM NaHPO4-NaH2PO4 (pH 5.5), 100mM NaCl, 50mM Na2SO4; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 1X3U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5W PHOSPHORYLATED FIXJ RECEIVER DOMAIN Deposited 1999-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, 2-METHYL-2,4-PENTANEDIOL, HEPES, TRITON X-100, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.244
1D5W PHOSPHORYLATED FIXJ RECEIVER DOMAIN Deposited 1999-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126) Chain C 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T2Q, A125L Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, 2-METHYL-2,4-PENTANEDIOL, HEPES, TRITON X-100, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.244
1DBW CRYSTAL STRUCTURE OF FIXJ-N Deposited 1999-11-03	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L	15P POLYETHYLENE GLYCOL (N=34) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 1.60 Å R-free 0.224
1DBW CRYSTAL STRUCTURE OF FIXJ-N Deposited 1999-11-03	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 1.60 Å R-free 0.224
1DCK STRUCTURE OF UNPHOSPHORYLATED FIXJ-N COMPLEXED WITH MN2+ Deposited 1999-11-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa） Fragment：N-TERMINAL DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L	MN MANGANESE (II) ION × 1 15P POLYETHYLENE GLYCOL (N=34) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.00 Å R-free 0.253
1DCK STRUCTURE OF UNPHOSPHORYLATED FIXJ-N COMPLEXED WITH MN2+ Deposited 1999-11-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–126（126 aa） Fragment：N-TERMINAL DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.00 Å R-free 0.253
1DCM STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A) Deposited 1999-11-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；PEG1500, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.00 Å R-free 0.335
1DCM STRUCTURE OF UNPHOSPHORYLATED FIXJ-N WITH AN ATYPICAL CONFORMER (MONOMER A) Deposited 1999-11-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–126（126 aa） Fragment：FIXJ RECEIVER DOMAIN (RESIDUES 1-126)	Mutation：T2Q, A125L	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；PEG1500, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 3.00 Å R-free 0.335

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FIXJ_RHIME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–79； UniProt 130–204

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	1x3u
Deposition date deposition_date	2005-05-10
Structure title title	Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot
Keywords keywords	HELIX-TURN-HELIX, Transcription; TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	11.92 Å
Radius of gyration Rg (electron density) rg_electron	11.64 Å
Forward intensity I(0) i0	442928000.00
Molecular weight molecular_weight	171400.0 kDa
Excluded volume excluded_volume	212680 Å³
Envelope volume envelope_volume	17743 Å³
Hydration-shell volume shell_volume	11368 Å³
Envelope diameter envelope_diameter	44.7 Å
Shell Rg shell_rg	19.12 Å
Envelope Rg envelope_rg	13.72 Å
Shape Rg shape_rg	11.64 Å
Total Rg total_rg	11.81 Å
Total atoms total_atoms	24400
Residues n_residues	1580
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	39.4 Å
Rg (real space) rg_real	11.88 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	4.4290e+08
I(0) uncertainty (real space) i0_real_error	4.7510e+06
Rg (reciprocal space) rg_reciprocal	11.89 Å
I(0) (reciprocal space) i0_reciprocal	442900000.0000
Solution quality estimate total_estimate	0.7877
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.5 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.206
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	172000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	1x3uA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Description description	Transcriptional regulatory protein fixJ
Molecular weight formula_weight	8580.9 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	24400

来源生物 organism	Sinorhizobium meliloti
NCBI Class编号 ncbi_taxonomy_id	382
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/x3/1x3u/1x3u.fit
pddf	/app/data/pr_computation/x3/1x3u/1x3u.pr.out
profile	/app/data/saxs_computation/x3/1x3u/1x3u.dat

Solution structure of the C-terminal transcriptional activator domain of FixJ from Sinorhizobium melilot

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

Transcriptional regulatory protein fixJ

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)