4km0

Crystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in complex with pyrimethamine

Method: X-RAY DIFFRACTION Dmax: 84.9 Å Quality: GOOD

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

Dihydrofolate reductase

Mycobacterium tuberculosis

UniProt P0A546

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 1–159 Not recorded CP6 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE × 1 ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.30 Å R-free 0.210
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–159 Not recorded CP6 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE × 1 ATR 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.30 Å R-free 0.210

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.

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYR_MYCTU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 21–179; UniProt 1–159 Author chain B; PDBConstruct 21–179; UniProt 1–159

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 4km0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4km0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4km0
Deposition date deposition_date2013-05-07
Structure title titleCrystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in complex with pyrimethamine
Keywords keywordsreductase, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.56
Radius of gyration Rg (electron density) rg_electron26.13
Forward intensity I(0) i025584800.00
Molecular weight molecular_weight37067.0 kDa
Excluded volume excluded_volume45569 ų
Envelope volume envelope_volume58081 ų
Hydration-shell volume shell_volume19459 ų
Envelope diameter envelope_diameter86.9
Shell Rg shell_rg31.95
Envelope Rg envelope_rg26.11
Shape Rg shape_rg26.14
Total Rg total_rg26.76
Total atoms total_atoms2604
Residues n_residues321
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 dmax84.9
Rg (real space) rg_real26.73
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real2.5580e+07
I(0) uncertainty (real space) i0_real_error3.4250e+05
Rg (reciprocal space) rg_reciprocal26.68
I(0) (reciprocal space) i0_reciprocal25580000.0000
Solution quality estimate total_estimate0.8556
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.1
Skewness Skewness skewness0.392
Kurtosis Kurtosis kurtosis-0.636
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3164000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.788; Smooth: 0.867

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4km0a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
Family Family familyc.71.1.0 — automated matches
Domain ID domain_idd4km0a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4km0b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamilyc.71.1 — Dihydrofolate reductase-like
Family Family familyc.71.1.0 — automated matches
Domain ID domain_idd4km0b2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4km0A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A
Domain ID domain_id4km0B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A

8. Citations (1)

9. Files and Curves (10)