1boo

PVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC)

Method: X-RAY DIFFRACTION Dmax: 62.2 Å Quality: EXCELLENT

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

PROTEIN (N-4 CYTOSINE-SPECIFIC METHYLTRANSFERASE PVU II)

Proteus vulgaris

UniProt P11409

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 14–336 Fragment:STARTING FROM THE INTERNAL TRANSLATION INITIATOR AT MET14 Mutation:N TERMIANL DELETION (RESIDUES 1-13) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.2;0.1 M HEPES PH 7.2, 0.2 M SODIUM ACETATE 20% POLYETHYLENE GLYCOL 400 Resolution 2.80 Å R-free 0.283

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name MTP2_PROVU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–323; UniProt 14–336

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 1boo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1boo
Deposition date deposition_date1998-07-31
Structure title titlePVUII DNA METHYLTRANSFERASE (CYTOSINE-N4-SPECIFIC)
Keywords keywords;TYPE II DNA-(CYTOSINE N4) METHYLTRANSFERASE, AMINO METHYLATION, SELENOMETHIONINE, MULTIWAVELENGTH ANOMALOUS DIFFRACTION, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.09
Radius of gyration Rg (electron density) rg_electron19.01
Forward intensity I(0) i016377600.00
Molecular weight molecular_weight31742.0 kDa
Excluded volume excluded_volume40191 ų
Envelope volume envelope_volume46385 ų
Hydration-shell volume shell_volume20305 ų
Envelope diameter envelope_diameter63.3
Shell Rg shell_rg25.56
Envelope Rg envelope_rg19.36
Shape Rg shape_rg18.97
Total Rg total_rg20.08
Total atoms total_atoms2245
Residues n_residues282
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 dmax62.2
Rg (real space) rg_real19.99
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real1.6380e+07
I(0) uncertainty (real space) i0_real_error1.9410e+05
Rg (reciprocal space) rg_reciprocal20.01
I(0) (reciprocal space) i0_reciprocal16380000.0000
Solution quality estimate total_estimate0.9059
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.441
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3157000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1booa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.11 — Type II DNA methylase

CATH v4.4 (1 domains)

Domain ID domain_id1booA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39

8. Citations (2)

9. Files and Curves (10)