1rqv

Spatial model of L7 dimer from E.coli with one hinge region in helical state

Method: SOLUTION NMR Dmax: 90.5 Å Quality: GOOD

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

50S ribosomal protein L7/L12

Escherichia coli

UniProt P0A7K2

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–120 Chain B; UniProt 1–120 Fragment:L7 dimer No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6.9;303 K;Ionic strength (raw mmCIF value) 0.15;Pressure ambient NMR sample composition:1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C | 90% H2O/10% D2O NMR sample composition:1mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C | 99.9% D2O NMR sample composition:1mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C; Tobacco virus alignment medium | 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.

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL7_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–120; UniProt 1–120 Author chain B; PDBConstruct 1–120; UniProt 1–120

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 1rqv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1rqv
Deposition date deposition_date2003-12-07
Structure title titleSpatial model of L7 dimer from E.coli with one hinge region in helical state
Keywords keywordsprotein L7/L12, ribosome; RIBOSOME
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier29.48
Radius of gyration Rg (electron density) rg_electron29.15
Forward intensity I(0) i09761870.00
Molecular weight molecular_weight24278.0 kDa
Excluded volume excluded_volume30746 ų
Envelope volume envelope_volume48989 ų
Hydration-shell volume shell_volume15552 ų
Envelope diameter envelope_diameter94.5
Shell Rg shell_rg33.29
Envelope Rg envelope_rg27.34
Shape Rg shape_rg29.11
Total Rg total_rg29.79
Total atoms total_atoms3476
Residues n_residues240
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 dmax90.5
Rg (real space) rg_real29.63
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real9.7620e+06
I(0) uncertainty (real space) i0_real_error1.5710e+05
Rg (reciprocal space) rg_reciprocal29.57
I(0) (reciprocal space) i0_reciprocal9761000.0000
Solution quality estimate total_estimate0.7845
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.4
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.896
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1108000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.527; Smooth: 0.571

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1rqva1
Class classa — All alpha proteins
Fold Fold folda.108 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily Superfamily superfamilya.108.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family Family familya.108.1.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Domain ID domain_idd1rqva2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.45 — ClpS-like
Superfamily Superfamily superfamilyd.45.1 — ClpS-like
Family Family familyd.45.1.1 — Ribosomal protein L7/12, C-terminal domain
Domain ID domain_idd1rqvb1
Class classa — All alpha proteins
Fold Fold folda.108 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily Superfamily superfamilya.108.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family Family familya.108.1.1 — Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Domain ID domain_idd1rqvb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.45 — ClpS-like
Superfamily Superfamily superfamilyd.45.1 — ClpS-like
Family Family familyd.45.1.1 — Ribosomal protein L7/12, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id1rqvA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily710 — Single helix bin
Domain ID domain_id1rqvA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1390 — Ribosomal Protein L30; Chain: A,
Homologous superfamily homologous superfamily10 — Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS
Domain ID domain_id1rqvB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily710 — Single helix bin
Domain ID domain_id1rqvB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1390 — Ribosomal Protein L30; Chain: A,
Homologous superfamily homologous superfamily10 — Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS

8. Citations (1)

9. Files and Curves (10)