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2qne

Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution

Method: X-RAY DIFFRACTION Dmax: 99.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Putative methyltransferase

Desulfitobacterium hafniense

UniProt Q24SP7

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 4–479 Chain B； UniProt 4–479 Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.30 Å R-free 0.204

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.

Other PDB Difference from Current Entry 2QNE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YCE Active site of MtgB, a glycine betaine methyltransferase from the MttB superfamily Deposited 2025-09-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 5–479（475 aa）
Chain B 5–479（475 aa）
Not recorded IMD IMIDAZOLE × 1 BET TRIMETHYL GLYCINE × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100 mM Imidazole, 1.0 M sodium citrate, pH 8.0
Resolution 2.35 Å R-free 0.216

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q24SP7_DESHY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–495； UniProt 4–479 Author chain B； PDBConstruct 20–495； UniProt 4–479

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 2qne

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2qne
Deposition date deposition_date2007-07-18
Structure title titleCrystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution
Keywords keywords;ZP_00558420.1, putative methyltransferase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Uncharacterized protein, UNKNOWN FUNCTION, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.81 Å
Radius of gyration Rg (electron density) rg_electron29.37 Å
Forward intensity I(0) i0177841000.00
Molecular weight molecular_weight104470.0 kDa
Excluded volume excluded_volume129080 ų
Envelope volume envelope_volume146940 ų
Hydration-shell volume shell_volume40836 ų
Envelope diameter envelope_diameter105.3 Å
Shell Rg shell_rg37.45 Å
Envelope Rg envelope_rg29.87 Å
Shape Rg shape_rg29.48 Å
Total Rg total_rg29.64 Å
Total atoms total_atoms7214
Residues n_residues913
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax99.8 Å
Rg (real space) rg_real29.81 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real1.7780e+08
I(0) uncertainty (real space) i0_real_error2.6870e+06
Rg (reciprocal space) rg_reciprocal29.81 Å
I(0) (reciprocal space) i0_reciprocal177800000.0000
Solution quality estimate total_estimate0.8763
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.9 Å
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.265
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha68130000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.912
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2qneA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily480 — Trimethylamine methyltransferase-like
Domain ID domain_id2qneB01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily480 — Trimethylamine methyltransferase-like
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8. Citations (1)

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9. Files and Curves (10)