5z3q

Crystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (2.55 Angstrom)

Method: X-RAY DIFFRACTION Dmax: 141.7 Å Quality: REASONABLE

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

PV-2C

Human poliovirus 1 Mahoney

UniProt P03300

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1243–1456 Chain C; UniProt 1243–1456 Chain D; UniProt 1243–1456 Chain E; UniProt 1243–1456 Fragment:UNP residues 1243-1456 Mutation:E207A, K209A,R149A ZN ZINC ION × 4 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;MgCl2 0.2M, MES 0.1M pH 6.5, 3%(v/v) PGE4000, Polypropylene glycol P 400 (9.2% v/v) , 0.5mM TECP HCl Resolution 2.54 Å R-free 0.265
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1243–1456 Fragment:UNP residues 1243-1456 Mutation:E207A, K209A,R149A ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;MgCl2 0.2M, MES 0.1M pH 6.5, 3%(v/v) PGE4000, Polypropylene glycol P 400 (9.2% v/v) , 0.5mM TECP HCl Resolution 2.54 Å R-free 0.265
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain H; UniProt 1243–1456 Fragment:UNP residues 1243-1456 Mutation:E207A, K209A,R149A ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;MgCl2 0.2M, MES 0.1M pH 6.5, 3%(v/v) PGE4000, Polypropylene glycol P 400 (9.2% v/v) , 0.5mM TECP HCl Resolution 2.54 Å R-free 0.265

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.

80 other PDB entries and 248 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_POL1M
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–214; UniProt 1243–1456 Author chain B; PDBConstruct 1–214; UniProt 1243–1456 Author chain C; PDBConstruct 1–214; UniProt 1243–1456 Author chain D; PDBConstruct 1–214; UniProt 1243–1456 Author chain E; PDBConstruct 1–214; UniProt 1243–1456 Author chain H; PDBConstruct 1–214; UniProt 1243–1456

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 5z3q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5z3q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5z3q
Deposition date deposition_date2018-01-08
Structure title titleCrystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (2.55 Angstrom)
Keywords keywordsATPase, viral protein; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.36
Radius of gyration Rg (electron density) rg_electron39.13
Forward intensity I(0) i0250700000.00
Molecular weight molecular_weight120930.0 kDa
Excluded volume excluded_volume148670 ų
Envelope volume envelope_volume214290 ų
Hydration-shell volume shell_volume47927 ų
Envelope diameter envelope_diameter153.4
Shell Rg shell_rg42.13
Envelope Rg envelope_rg39.11
Shape Rg shape_rg39.01
Total Rg total_rg39.70
Total atoms total_atoms16567
Residues n_residues1086
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 dmax141.7
Rg (real space) rg_real39.67
Rg uncertainty (real space) rg_real_error1.62
I(0) (real space) i0_real2.5070e+08
I(0) uncertainty (real space) i0_real_error4.8710e+06
Rg (reciprocal space) rg_reciprocal39.48
I(0) (reciprocal space) i0_reciprocal250600000.0000
Solution quality estimate total_estimate0.6232
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.1
Skewness Skewness skewness0.562
Kurtosis Kurtosis kurtosis0.070
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha26690000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.890; Smooth: 0.812

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)