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1b5d

DCMP Hydroxymethylase from T4 (Intact)

Method: X-RAY DIFFRACTION Dmax: 79.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–246 Chain B； UniProt 1–246 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–246 Chain B； UniProt 1–246 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

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 1B5D 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 ligand/ion 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
1B5E DCMP HYDROXYMETHYLASE FROM T4 Deposited 1999-01-06 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 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 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）
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 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）
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
6L18 XFEL structure of T4dCH D179N mutant complex with natively expressed dTMP Deposited 2019-09-27 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）
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

5 other PDB entries and 6 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 Author chain B； 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 1b5d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b5d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b5d
Deposition date deposition_date1999-01-06
Structure title titleDCMP Hydroxymethylase from T4 (Intact)
Keywords keywordsHYDROXYMETHYLASE, DNTP SYNTHESIZING COMPLEX, 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_guinier23.63 Å
Radius of gyration Rg (electron density) rg_electron22.74 Å
Forward intensity I(0) i054186800.00
Molecular weight molecular_weight57551.0 kDa
Excluded volume excluded_volume71947 ų
Envelope volume envelope_volume83465 ų
Hydration-shell volume shell_volume29669 ų
Envelope diameter envelope_diameter81.1 Å
Shell Rg shell_rg30.92 Å
Envelope Rg envelope_rg23.11 Å
Shape Rg shape_rg22.76 Å
Total Rg total_rg23.59 Å
Total atoms total_atoms4058
Residues n_residues492
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 dmax79.2 Å
Rg (real space) rg_real23.51 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real5.4190e+07
I(0) uncertainty (real space) i0_real_error6.8550e+05
Rg (reciprocal space) rg_reciprocal23.54 Å
I(0) (reciprocal space) i0_reciprocal54190000.0000
Solution quality estimate total_estimate0.7091
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.7 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.300
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18550000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 1.000; Smooth: 0.989
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b5da_
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
Domain ID domain_idd1b5db_
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 (2 domains)

Domain ID domain_id1b5dA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology572 — Thymidylate Synthase; Chain A
Homologous superfamily homologous superfamily10 — Thymidylate synthase/dCMP hydroxymethylase domain
Domain ID domain_id1b5dB00
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)