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1j56

MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS

Method: SOLUTION NMR Dmax: 47.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NITROGEN REGULATION PROTEIN NR(I)

Salmonella typhimurium

UniProt P41789

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 1J56 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
1KRW SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN Deposited 2002-01-10 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 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
1KRX SOLUTION STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURES 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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 1j56

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1j56
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1j56
Deposition date deposition_date2002-01-10
Structure title titleMINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS
Keywords keywordstwo component signal transduction, receiver domain, BeF3, phosphorylation, Bacterial nitrogen regulatory protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.02 Å
Radius of gyration Rg (electron density) rg_electron13.32 Å
Forward intensity I(0) i03779600.00
Molecular weight molecular_weight13666.0 kDa
Excluded volume excluded_volume17134 ų
Envelope volume envelope_volume19015 ų
Hydration-shell volume shell_volume11950 ų
Envelope diameter envelope_diameter46.0 Å
Shell Rg shell_rg19.33 Å
Envelope Rg envelope_rg13.81 Å
Shape Rg shape_rg13.29 Å
Total Rg total_rg14.74 Å
Total atoms total_atoms1919
Residues n_residues124
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax47.7 Å
Rg (real space) rg_real14.90 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real3.7800e+06
I(0) uncertainty (real space) i0_real_error3.9970e+04
Rg (reciprocal space) rg_reciprocal14.92 Å
I(0) (reciprocal space) i0_reciprocal3780000.0000
Solution quality estimate total_estimate0.8816
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.6 Å
Skewness Skewness skewness0.090
Kurtosis Kurtosis kurtosis-0.366
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha920900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.831; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.977
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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_idd1j56a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.1 — CheY-like
Family Family familyc.23.1.1 — CheY-related

CATH v4.4 (1 domains)

Domain ID domain_id1j56A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (3)

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9. Files and Curves (10)