5bkn

Crystallographic structure of a cubic crystal form of STMV (84.5 degree rotation) grown from chloride

Method: X-RAY DIFFRACTION Dmax: 176.7 Å Quality: GOOD

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

Coat protein

OrganismNot specified

UniProt P17574

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–RNA Homooligomer Protein × 60 RNA 57 PDB declaration: 117-meric(117) Consistent with all polymer counts Chain A; UniProt 1–159 Chain B; UniProt 1–159 Chain C; UniProt 1–159 Chain D; UniProt 1–159 Chain E; UniProt 1–159 Chain F; UniProt 1–159 Chain G; UniProt 1–159 Chain GG; UniProt 1–159 Chain H; UniProt 1–159 Chain HH; UniProt 1–159 Chain I; UniProt 1–159 Chain II; UniProt 1–159 Chain J; UniProt 1–159 Chain JJ; UniProt 1–159 Chain K; UniProt 1–159 Chain KK; UniProt 1–159 Chain L; UniProt 1–159 Chain M; UniProt 1–159 Chain N; UniProt 1–159 Chain O; UniProt 1–159 Not recorded ;RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3') ; × 9 ;RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') ; × 3 ;RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') ; × 3 ;RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') ; × 12 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') ; × 6 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') ; × 3 ;RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') ; × 6 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') ; × 9 ;RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3') ; × 3 ;RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') ; × 3 CL CHLORIDE ION × 78 MG MAGNESIUM ION × 42 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;279 K;Crystals were grown by sitting drop vapor diffusion in Cryschem plates using .6 ml reservoirs. The drops were composed of equal volumes of a 5 mg/ml virus stock solution of 0.1 M phosphate at pH 6.5, and the reservoir solution, which was 8% NaCl w/v in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C. Resolution 3.00 Å R-free 0.255

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.

13 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COAT_STMV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–159; UniProt 1–159 Author chain B; PDBConstruct 1–159; UniProt 1–159 Author chain C; PDBConstruct 1–159; UniProt 1–159 Author chain D; PDBConstruct 1–159; UniProt 1–159 Author chain E; PDBConstruct 1–159; UniProt 1–159 Author chain F; PDBConstruct 1–159; UniProt 1–159 Author chain G; PDBConstruct 1–159; UniProt 1–159 Author chain GG; PDBConstruct 1–159; UniProt 1–159 Author chain H; PDBConstruct 1–159; UniProt 1–159 Author chain HH; PDBConstruct 1–159; UniProt 1–159 Author chain I; PDBConstruct 1–159; UniProt 1–159 Author chain II; PDBConstruct 1–159; UniProt 1–159 Author chain J; PDBConstruct 1–159; UniProt 1–159 Author chain JJ; PDBConstruct 1–159; UniProt 1–159 Author chain K; PDBConstruct 1–159; UniProt 1–159 Author chain KK; PDBConstruct 1–159; UniProt 1–159 Author chain L; PDBConstruct 1–159; UniProt 1–159 Author chain M; PDBConstruct 1–159; UniProt 1–159 Author chain N; PDBConstruct 1–159; UniProt 1–159 Author chain O; PDBConstruct 1–159; UniProt 1–159

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 5bkn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5bkn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5bkn
Deposition date deposition_date2021-03-20
Structure title titleCrystallographic structure of a cubic crystal form of STMV (84.5 degree rotation) grown from chloride
Keywords keywordsanions, RNA, ion channel, fivefold vertex, crystallization, VIRUS; VIRUS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier56.11
Radius of gyration Rg (electron density) rg_electron56.72
Forward intensity I(0) i02343340000.00
Molecular weight molecular_weight366610.0 kDa
Excluded volume excluded_volume442650 ų
Envelope volume envelope_volume817150 ų
Hydration-shell volume shell_volume116950 ų
Envelope diameter envelope_diameter173.0
Shell Rg shell_rg63.40
Envelope Rg envelope_rg54.37
Shape Rg shape_rg56.75
Total Rg total_rg56.79
Total atoms total_atoms48637
Residues n_residues3042
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 dmax176.7
Rg (real space) rg_real55.93
Rg uncertainty (real space) rg_real_error1.46
I(0) (real space) i0_real2.3430e+09
I(0) uncertainty (real space) i0_real_error4.6170e+07
Rg (reciprocal space) rg_reciprocal56.23
I(0) (reciprocal space) i0_reciprocal2344000000.0000
Solution quality estimate total_estimate0.8764
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.1
Skewness Skewness skewness0.109
Kurtosis Kurtosis kurtosis-0.704
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha123600000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.517

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

8. Citations (1)

9. Files and Curves (10)