2fvr

A Structural Study of the CA Dinucleotide Step in the Integrase Processing Site of Moloney Murine Leukemia Virus

Method: X-RAY DIFFRACTION Dmax: 91.6 Å Quality: GOOD

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

reverse transcriptase

Moloney murine leukemia virus

UniProt P03355

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 144–398 Not recorded 5'-D(*TP*CP*TP*TP*TP*CP*AP*TP*AP*TP*GP*AP*AP*AP*GP*A)-3' × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;PEG 4000, magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.259

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.

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_MLVMO
Isoform
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–255; UniProt 144–398

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 2fvr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2fvr
Deposition date deposition_date2006-01-31
Structure title titleA Structural Study of the CA Dinucleotide Step in the Integrase Processing Site of Moloney Murine Leukemia Virus
Keywords keywordsLTR, MMLV, integrase, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.58
Radius of gyration Rg (electron density) rg_electron24.53
Forward intensity I(0) i022050000.00
Molecular weight molecular_weight33798.0 kDa
Excluded volume excluded_volume41342 ų
Envelope volume envelope_volume56525 ų
Hydration-shell volume shell_volume20510 ų
Envelope diameter envelope_diameter90.8
Shell Rg shell_rg29.35
Envelope Rg envelope_rg25.63
Shape Rg shape_rg24.44
Total Rg total_rg25.34
Total atoms total_atoms2366
Residues n_residues271
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 dmax91.6
Rg (real space) rg_real26.80
Rg uncertainty (real space) rg_real_error0.79
I(0) (real space) i0_real2.2050e+07
I(0) uncertainty (real space) i0_real_error3.0570e+05
Rg (reciprocal space) rg_reciprocal26.73
I(0) (reciprocal space) i0_reciprocal22050000.0000
Solution quality estimate total_estimate0.8555
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary26.0
Skewness Skewness skewness0.502
Kurtosis Kurtosis kurtosis-0.234
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1645000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.763; Smooth: 0.873

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2fvra_
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.8.1.2 — Reverse transcriptase

CATH v4.4 (2 domains)

Domain ID domain_id2fvrA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id2fvrA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology10 — HIV Type 1 Reverse Transcriptase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — HIV Type 1 Reverse Transcriptase, subunit A, domain 1

8. Citations (1)

9. Files and Curves (10)