1a04

THE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL IN THE MONOCLINIC C2 CRYSTAL FORM

Method: X-RAY DIFFRACTION Dmax: 89.7 Å Quality: GOOD

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

NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL

Escherichia coli

UniProt P10957

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 2–216 Fragment:RESIDUES 2 - 216 OF THE WILD TYPE NARL No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.6;277 K;THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M TRIS.HCL (PH=8.5), 0.2 M SODIUM ACETATE, AND 30% POLYETHYLENE GLYCOL (PEG) 4000. SITTING DROPS CONTAINING 20 ML OF MIXTURE WERE EQUILIBRATED BY VAPOR DIFFUSION AT 4 DEGREES AGAINST 20 ML OF THE RESERVOIR SOLUTION. CRYSTALS BEGAN TO APPEAR AS CLUSTERS OF PLATES AFTER 11-15 DAYS., vapor diffusion - sitting drop, temperature 277K Resolution 2.20 Å R-free 0.267
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2–216 Fragment:RESIDUES 2 - 216 OF THE WILD TYPE NARL No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.6;277 K;THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M TRIS.HCL (PH=8.5), 0.2 M SODIUM ACETATE, AND 30% POLYETHYLENE GLYCOL (PEG) 4000. SITTING DROPS CONTAINING 20 ML OF MIXTURE WERE EQUILIBRATED BY VAPOR DIFFUSION AT 4 DEGREES AGAINST 20 ML OF THE RESERVOIR SOLUTION. CRYSTALS BEGAN TO APPEAR AS CLUSTERS OF PLATES AFTER 11-15 DAYS., vapor diffusion - sitting drop, temperature 277K Resolution 2.20 Å R-free 0.267

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.

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NARL_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–215; UniProt 2–216 Author chain B; PDBConstruct 1–215; UniProt 2–216

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 1a04

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a04
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1a04
Deposition date deposition_date1997-12-08
Structure title titleTHE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL IN THE MONOCLINIC C2 CRYSTAL FORM
Keywords keywordsSIGNAL TRANSDUCTION PROTEIN, RESPONSE REGULATORS, TWO-COMPONENT SYSTEMS; SIGNAL TRANSDUCTION PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.29
Radius of gyration Rg (electron density) rg_electron25.68
Forward intensity I(0) i033681300.00
Molecular weight molecular_weight45343.0 kDa
Excluded volume excluded_volume57225 ų
Envelope volume envelope_volume70237 ų
Hydration-shell volume shell_volume23608 ų
Envelope diameter envelope_diameter91.3
Shell Rg shell_rg31.75
Envelope Rg envelope_rg25.61
Shape Rg shape_rg25.66
Total Rg total_rg26.47
Total atoms total_atoms3174
Residues n_residues410
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.7
Rg (real space) rg_real26.40
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real3.3680e+07
I(0) uncertainty (real space) i0_real_error4.0970e+05
Rg (reciprocal space) rg_reciprocal26.37
I(0) (reciprocal space) i0_reciprocal33680000.0000
Solution quality estimate total_estimate0.8634
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary25.4
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis-0.441
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha10360000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1a04a1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family familya.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)
Domain ID domain_idd1a04a2
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
Domain ID domain_idd1a04b1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.6 — C-terminal effector domain of the bipartite response regulators
Family Family familya.4.6.2 — GerE-like (LuxR/UhpA family of transcriptional regulators)
Domain ID domain_idd1a04b2
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 (4 domains)

Domain ID domain_id1a04A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1a04A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id1a04B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id1a04B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

8. Citations (2)

9. Files and Curves (10)