SAXSdb — 1krx

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

NITROGEN REGULATION PROTEIN NR(I)

Salmonella typhimurium

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：N-terminal domain: Receiver domain, Residues 1-124	BEF BERYLLIUM TRIFLUORIDE ION × 1	SOLUTION NMR NMR measurement conditions：pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions：pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions：pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions：pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR sample composition：U-15N, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition：U-15N, 13C, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition：10% 13C, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition：U-15N, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O, 30mg/ml phage pf1 \| 95% H2O/5% 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 1KRX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DC7 STRUCTURE OF A TRANSIENTLY PHOSPHORYLATED "SWITCH" IN BACTERIAL SIGNAL TRANSDUCTION Deposited 1999-11-04	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa） Fragment：N-TERMINAL RECEIVER DOMAIN(1-124)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.75；298 K；Ionic strength (raw mmCIF value) 50 mM；Pressure 1 NMR sample composition 1 MM NTRC(1-124) U-15N; 50 MM SODIUM PHOSPHATE, PH 6.75 NMR sample composition 1 MM NTRC(1-124) U-15N/13C; 50 MM SODIUM PHOSPHATE, PH 6.75 NMR sample composition 1 MM NTRC(1-124) U-15N; 50 MM SODIUM PHOSPHATE, PH 6.75	Resolution not provided
1DC8 STRUCTURE OF A TRANSIENTLY PHOSPHORYLATED "SWITCH" IN BACTERIAL SIGNAL TRANSDUCTION Deposited 1999-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa） Fragment：N-TERMINAL RECEIVER DOMAIN(1-124)	Mutation：D54(ASQ) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.75；298 K；Ionic strength (raw mmCIF value) 250-500 mM；Pressure 1 NMR sample composition 0.3 MM NTRC(1-124) U-15N; 200 MM SODIUM PHOSPHATE, PH 6.75; 50 MM MAGNESIUM CHLORIDE; 200 MM CARBAMOYLPHOSPHATE NMR sample composition 0.3 MM NTRC(1-124) U-15N,13C; 200 MM SODIUM PHOSPHATE, PH 6.75; 50 MM MAGNESIUM CHLORIDE; 200 MM CARBAMOYLPHOSPHATE NMR sample composition 0.3 MM NTRC(1-124) U-15N; 200 MM SODIUM PHOSPHATE, PH 6.75; 50 MM MAGNESIUM CHLORIDE; 200 MM CARBAMOYLPHOSPHATE	Resolution not provided
1J56 MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS Deposited 2002-01-10	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa） Fragment：N-terminal domain: Receiver domain, Residues 1-124	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1	SOLUTION NMR NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR sample composition U-15N; 1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition U-15N, 13C;1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 10% 13C;1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition U-15N; 1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O; 30mg/ml phage pf1 \| 95% H2O/5% D2O	Resolution not provided
1KRW SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN Deposited 2002-01-10	Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa） Fragment：N-terminal domain: Receiver domain, Residues 1-124	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR measurement conditions pH 6.75；303 K；Ionic strength (raw mmCIF value) 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF；Pressure ambient NMR sample composition U-15N, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition U-15N, 13C, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 10% 13C, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition U-15N, 1.1-1.5mM NtrC receiver domain(1-124), 50mM sodium phosphate buffer(pH6.75), 50mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF, 95% H2O, 5% D2O, 30mg/ml phage pf1 \| 95% H2O/5% D2O	Resolution not provided
1NTC SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF NTRC WITH THREE ALANINE SUBSTITUTIONS Deposited 1999-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 379–469（91 aa） Chain B 379–469（91 aa）	Mutation：R456A, N457A, R461A Mutation：R456A, N457A, R461A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；307 K；Ionic strength (raw mmCIF value) 0.07；Pressure 1 NMR sample composition 90% WATER/10% D2O	Resolution not provided
1NTR SOLUTION STRUCTURE OF THE N-TERMINAL RECEIVER DOMAIN OF NTRC Deposited 1994-09-16	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

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

View Construct and Data Evidence

UniProt name	NTRC_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； 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	1krx
Deposition date deposition_date	2002-01-10
Structure title title	SOLUTION STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURES INCORPORATING ACTIVE SITE CONTACTS
Keywords keywords	two component signal transduction, receiver domain, BeF3, phosphorylation, Bacterial nitrogen regulatory protein, SIGNALING PROTEIN; SIGNALING PROTEIN
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	13.72 Å
Radius of gyration Rg (electron density) rg_electron	13.19 Å
Forward intensity I(0) i0	1713010000.00
Molecular weight molecular_weight	355310.0 kDa
Excluded volume excluded_volume	445480 Å³
Envelope volume envelope_volume	27252 Å³
Hydration-shell volume shell_volume	14943 Å³
Envelope diameter envelope_diameter	49.5 Å
Shell Rg shell_rg	21.40 Å
Envelope Rg envelope_rg	15.50 Å
Shape Rg shape_rg	13.16 Å
Total Rg total_rg	13.40 Å
Total atoms total_atoms	49894
Residues n_residues	3224
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	43.7 Å
Rg (real space) rg_real	13.61 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	1.7130e+09
I(0) uncertainty (real space) i0_real_error	1.5390e+07
Rg (reciprocal space) rg_reciprocal	13.62 Å
I(0) (reciprocal space) i0_reciprocal	1713000000.0000
Solution quality estimate total_estimate	0.7347
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.022
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	331800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.987; Smooth: 0.994

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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1krxa_
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.23.1.1 — CheY-related

CATH v4.4 (1 domains)

Domain ID domain_id	1krxA00
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 (3)

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Description description	NITROGEN REGULATION PROTEIN NR(I)
Molecular weight formula_weight	13636.6 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	49894

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli BL21

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/kr/1krx/1krx.fit
pddf	/app/data/pr_computation/kr/1krx/1krx.pr.out
profile	/app/data/saxs_computation/kr/1krx/1krx.dat

SOLUTION STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURES INCORPORATING ACTIVE SITE CONTACTS

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

NITROGEN REGULATION PROTEIN NR(I)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)