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1rip

RIBOSOMAL PROTEIN S17: CHARACTERIZATION OF THE THREE-DIMENSIONAL STRUCTURE BY 1H-AND 15N-NMR

Method: SOLUTION NMR Dmax: 52.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBOSOMAL PROTEIN S17

Geobacillus stearothermophilus

UniProt P23828

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 5–84 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions 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 1RIP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric
Chain G 1–93（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.50 Å
1QD7 PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT Deposited 1999-07-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: decameric
Chain I 5–86（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；VAPOUR DIFFUSION AT 277 K, MPD, VAPOR DIFFUSION
Resolution 5.50 Å

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

View Construct and Data Evidence
UniProt name RS17_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–80； UniProt 5–84

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 1rip

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1rip
Deposition date deposition_date1993-08-17
Structure title titleRIBOSOMAL PROTEIN S17: CHARACTERIZATION OF THE THREE-DIMENSIONAL STRUCTURE BY 1H-AND 15N-NMR
Keywords keywordsRIBOSOMAL PROTEIN; RIBOSOMAL 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_guinier14.62 Å
Radius of gyration Rg (electron density) rg_electron14.15 Å
Forward intensity I(0) i045508400.00
Molecular weight molecular_weight57254.0 kDa
Excluded volume excluded_volume73068 ų
Envelope volume envelope_volume27774 ų
Hydration-shell volume shell_volume14492 ų
Envelope diameter envelope_diameter54.8 Å
Shell Rg shell_rg22.03 Å
Envelope Rg envelope_rg16.71 Å
Shape Rg shape_rg14.12 Å
Total Rg total_rg14.81 Å
Total atoms total_atoms8364
Residues n_residues486
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 dmax52.6 Å
Rg (real space) rg_real14.65 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real4.5510e+07
I(0) uncertainty (real space) i0_real_error5.0760e+05
Rg (reciprocal space) rg_reciprocal14.65 Å
I(0) (reciprocal space) i0_reciprocal45510000.0000
Solution quality estimate total_estimate0.7766
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.3 Å
Skewness Skewness skewness0.341
Kurtosis Kurtosis kurtosis-0.408
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha410200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.717; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ripa_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.4 — Nucleic acid-binding proteins
Family Family familyb.40.4.5 — Cold shock DNA-binding domain-like

CATH v4.4 (1 domains)

Domain ID domain_id1ripA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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8. Citations (3)

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9. Files and Curves (10)