4jri

Crystal Structure of Escherichia coli Hfq Proximal Edge Mutant

Method: X-RAY DIFFRACTION Dmax: 85.9 Å Quality: GOOD

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

Protein hfq

Escherichia coli

UniProt P0A6X3

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–69 Chain B; UniProt 2–69 Fragment:UNP residues 2-69 Mutation:F39W No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.83 Å R-free 0.257
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 2–69 Chain D; UniProt 2–69 Fragment:UNP residues 2-69 Mutation:F39W No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.83 Å R-free 0.257

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.

14 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name P0A6X3_ECO1E
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–68; UniProt 2–69 Author chain B; PDBConstruct 1–68; UniProt 2–69 Author chain C; PDBConstruct 1–68; UniProt 2–69 Author chain D; PDBConstruct 1–68; UniProt 2–69

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 4jri

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4jri
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4jri
Deposition date deposition_date2013-03-21
Structure title titleCrystal Structure of Escherichia coli Hfq Proximal Edge Mutant
Keywords keywordsRiboregulator, Post-transcriptional regulator, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.18
Radius of gyration Rg (electron density) rg_electron23.91
Forward intensity I(0) i013448400.00
Molecular weight molecular_weight29102.0 kDa
Excluded volume excluded_volume37235 ų
Envelope volume envelope_volume45781 ų
Hydration-shell volume shell_volume17707 ų
Envelope diameter envelope_diameter87.7
Shell Rg shell_rg28.45
Envelope Rg envelope_rg24.18
Shape Rg shape_rg23.93
Total Rg total_rg24.52
Total atoms total_atoms2055
Residues n_residues255
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 dmax85.9
Rg (real space) rg_real24.49
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.3450e+07
I(0) uncertainty (real space) i0_real_error1.9610e+05
Rg (reciprocal space) rg_reciprocal24.42
I(0) (reciprocal space) i0_reciprocal13450000.0000
Solution quality estimate total_estimate0.7871
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.5
Skewness Skewness skewness0.577
Kurtosis Kurtosis kurtosis-0.306
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4449000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.604; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.491; Smooth: 0.925

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_idd4jria_
Class classb — All beta proteins
Fold Fold foldb.38 — Sm-like fold
Superfamily Superfamily superfamilyb.38.1 — Sm-like ribonucleoproteins
Family Family familyb.38.1.2 — Pleiotropic translational regulator Hfq
Domain ID domain_idd4jrib_
Class classb — All beta proteins
Fold Fold foldb.38 — Sm-like fold
Superfamily Superfamily superfamilyb.38.1 — Sm-like ribonucleoproteins
Family Family familyb.38.1.2 — Pleiotropic translational regulator Hfq
Domain ID domain_idd4jric_
Class classb — All beta proteins
Fold Fold foldb.38 — Sm-like fold
Superfamily Superfamily superfamilyb.38.1 — Sm-like ribonucleoproteins
Family Family familyb.38.1.2 — Pleiotropic translational regulator Hfq
Domain ID domain_idd4jrid_
Class classb — All beta proteins
Fold Fold foldb.38 — Sm-like fold
Superfamily Superfamily superfamilyb.38.1 — Sm-like ribonucleoproteins
Family Family familyb.38.1.2 — Pleiotropic translational regulator Hfq

CATH v4.4 (4 domains)

Domain ID domain_id4jriA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100
Domain ID domain_id4jriB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100
Domain ID domain_id4jriC00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100
Domain ID domain_id4jriD00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily100

8. Citations (1)

9. Files and Curves (10)