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6l18

XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP

Method: X-RAY DIFFRACTION Dmax: 64.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Deoxycytidylate 5-hydroxymethyltransferase

Enterobacteria phage T4

UniProt P08773

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 1–246 Mutation：D179N TMP THYMIDINE-5'-PHOSPHATE × 2 IOD IODIDE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：SMALL TUBES；pH 8.5；293 K；2 ul of 1.0 M Tris-HCl pH 8.5 2 ul of 1.0 M NaI 17 ul of C6H5Na3 2H2O 10 ul of 40mg/ml D179N mutant protein Resolution 1.90 Å R-free 0.191

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 6L18 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B49 DCMP HYDROXYMETHYLASE FROM T4 (PHOSPHATE-BOUND) Deposited 1999-01-06 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 1–246（246 aa）
Chain C 1–246（246 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.30 Å R-free 0.202
1B5D DCMP Hydroxymethylase from T4 (Intact) Deposited 1999-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Not recorded DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.20 Å R-free 0.208
1B5D DCMP Hydroxymethylase from T4 (Intact) Deposited 1999-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Not recorded DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.20 Å R-free 0.208
1B5E DCMP HYDROXYMETHYLASE FROM T4 Deposited 1999-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Not recorded DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.60 Å R-free 0.208
1B5E DCMP HYDROXYMETHYLASE FROM T4 Deposited 1999-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–246（246 aa）
Chain B 1–246（246 aa）
Not recorded DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.60 Å R-free 0.208
6A9A Ternary complex crystal structure of dCH with dCMP and THF Deposited 2018-07-12 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 1–246（246 aa）
Mutation：C148S, D179N IOD IODIDE ION × 2 DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 2 THG (6S)-5,6,7,8-TETRAHYDROFOLATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Tris-HCl pH 8.0, Sodium citrate
Resolution 1.90 Å R-free 0.187
6A9B T4 dCMP hydroxymethylase structure solved by I-SAD using a home source Deposited 2018-07-12 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 1–246（246 aa）
Not recorded IOD IODIDE ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M Tris-HCl pH 8.5 0.96 M sodium citrate
Resolution 2.01 Å R-free 0.192

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DCHM_BPT4
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–246； UniProt 1–246

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 6l18

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6l18
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6l18
Deposition date deposition_date2019-09-27
Structure title titleXFEL structure of T4dCH D179N mutant complex with natively expressed dTMP
Keywords keywordsXFEL, Room temperature, dTMP, Complex, Natively inhibited, Hydroxymethylase, 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_guinier20.02 Å
Radius of gyration Rg (electron density) rg_electron19.01 Å
Forward intensity I(0) i014926900.00
Molecular weight molecular_weight28940.0 kDa
Excluded volume excluded_volume36087 ų
Envelope volume envelope_volume43242 ų
Hydration-shell volume shell_volume19195 ų
Envelope diameter envelope_diameter65.9 Å
Shell Rg shell_rg25.14 Å
Envelope Rg envelope_rg19.27 Å
Shape Rg shape_rg18.97 Å
Total Rg total_rg20.03 Å
Total atoms total_atoms2032
Residues n_residues246
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 dmax64.6 Å
Rg (real space) rg_real19.94 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real1.4930e+07
I(0) uncertainty (real space) i0_real_error1.8160e+05
Rg (reciprocal space) rg_reciprocal19.96 Å
I(0) (reciprocal space) i0_reciprocal14930000.0000
Solution quality estimate total_estimate0.8979
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.7 Å
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2715000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.995
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6l18a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.117 — Thymidylate synthase/dCMP hydroxymethylase
Superfamily Superfamily superfamilyd.117.1 — Thymidylate synthase/dCMP hydroxymethylase
Family Family familyd.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (1 domains)

Domain ID domain_id6l18A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
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8. Citations (1)

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9. Files and Curves (10)