2xxd

HCV-JFH1 NS5B polymerase structure at 1.9 angstrom

Method: X-RAY DIFFRACTION Dmax: 74.8 Å Quality: EXCELLENT

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

RNA-DIRECTED RNA POLYMERASE

HEPATITIS C VIRUS

UniProt Q99IB8

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 2443–3005 Fragment:CATALYTIC DOMAIN, RESIDUES 2443-3005 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;0.2M SODIUM PHOSPHATE PH 6.5, 12% PEG3350. Resolution 1.88 Å R-free 0.206

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.

31 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HCVJF
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–563; UniProt 2443–3005

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 2xxd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2xxd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2xxd
Deposition date deposition_date2010-11-10
Structure title titleHCV-JFH1 NS5B polymerase structure at 1.9 angstrom
Keywords keywordsTRANSFERASE, HEPACIVIRUS, NONSTRUCTURAL PROTEINS, REPLICATION, DE NOVO INITIATION, PRIMING; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.11
Radius of gyration Rg (electron density) rg_electron23.99
Forward intensity I(0) i066185600.00
Molecular weight molecular_weight62889.0 kDa
Excluded volume excluded_volume78568 ų
Envelope volume envelope_volume93311 ų
Hydration-shell volume shell_volume31524 ų
Envelope diameter envelope_diameter79.0
Shell Rg shell_rg31.86
Envelope Rg envelope_rg23.93
Shape Rg shape_rg23.96
Total Rg total_rg24.94
Total atoms total_atoms4411
Residues n_residues563
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 dmax74.8
Rg (real space) rg_real24.96
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real6.6190e+07
I(0) uncertainty (real space) i0_real_error8.2110e+05
Rg (reciprocal space) rg_reciprocal25.01
I(0) (reciprocal space) i0_reciprocal66190000.0000
Solution quality estimate total_estimate0.9134
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.0
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.557
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12380000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2xxda_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.4 — RNA-dependent RNA-polymerase

8. Citations (1)

9. Files and Curves (10)