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2l28

Solution structure of lactobacillus casei dihydrofolate reductase apo-form, 25 conformers

Method: SOLUTION NMR Dmax: 50.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydrofolate reductase

Lactobacillus casei

UniProt P00381

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 2–163 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；288 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition：2 mM entity-1, 100 mM potassium chloride-2, 50 mM potassium phosphate-3, 0.1 % sodium azide-4, 100% D2O | 100% D2O NMR sample composition：1 mM [U-99% 13C; U-99% 15N] entity-5, 100 mM potassium chloride-6, 50 mM potassium phosphate-7, 0.1 % sodium azide-8, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-99% 15N] entity-9, 100 mM potassium chloride-10, 50 mM potassium phosphate-11, 0.1 % sodium azide-12, 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition：1 mM [U-99% 15N] entity-13, 100 mM potassium chloride-14, 50 mM potassium phosphate-15, 0.1 % sodium azide-16, 5 % DMPC/DHPC-17, 95% H2O/5% D2O | 95% H2O/5% D2O Resolution not provided

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 2L28 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AO8 DIHYDROFOLATE REDUCTASE COMPLEXED WITH METHOTREXATE, NMR, 21 STRUCTURES Deposited 1997-07-22 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded MTX METHOTREXATE × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 150 mM
Resolution not provided
1BZF NMR SOLUTION STRUCTURE AND DYNAMICS OF THE COMPLEX OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE WITH THE NEW LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE, 22 STRUCTURES Deposited 1998-10-28 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded TMQ TRIMETREXATE × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 550 mM；Pressure 1
NMR sample composition 90% H2O/10% D2O, 100% D2O
Resolution not provided
1DIS DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEX WITH BRODIMOPRIM-4,6-DICARBOXYLATE Deposited 1995-08-01 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded BDM BRODIMOPRIM-4,6-DICARBOXYLATE × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1DIU DIHYDROFOLATE REDUCTASE (E.C.1.5.1.3) COMPLEX WITH BRODIMOPRIM-4,6-DICARBOXYLATE Deposited 1995-08-01 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded BDM BRODIMOPRIM-4,6-DICARBOXYLATE × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1LUD SOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIMETHOPRIM AND NADPH, 24 STRUCTURES Deposited 2002-05-22 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 TRR 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient
NMR sample composition 3mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer | 90% H2O/10% D2O
NMR sample composition 3 mM DHFR/TMP/NADPH, 50 mM phosphate buffer | 100% D2O
NMR sample composition 0.5mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer, 5% DMPC/DHPC (3:1) | 90% H2O/10% D2O
NMR sample composition 0.25mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer, 5% C12E5/hexanol | 90% H2O/10% D2O
Resolution not provided
2HM9 Solution structure of dihydrofolate reductase complexed with trimethoprim, 33 structures Deposited 2006-07-11 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded TRR 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure ambient
NMR sample composition 0.5mM DHFR-15N/TMP, 50mM phosphate buffer, 5% DMPC/DHPC (3:1), 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM DHFR-15N/TMP, 50mM phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM DHFR-15N/TMP, 50mM phosphate buffer, 100% D2O | 100% D2O
Resolution not provided
2HQP Solution structure of L.casei dihydrofolate reductase complexed with NADPH, 32 structures Deposited 2006-07-19 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure ambient
NMR sample composition 0.5mM DHFR-15N/NADPH, 50mM phosphate buffer, 5% DMPC/DHPC, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM DHFR-15N/NADPH, 50mM phosphate buffer, 100% H2O | 100% H2O
NMR sample composition 1mM DHFR-15N/NADPH, 50mM phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2LF1 Solution structure of L. casei dihydrofolate reductase complexed with NADPH, 30 structures Deposited 2011-06-28 Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–163（162 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 2 mM [U-99% 13C; U-99% 15N] DHFR, 2 mM NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 100 mM potassium chloride, 50 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2 mM [U-99% 13C; U-99% 15N] DHFR, 2 mM NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 100 mM potassium chloride, 50 mM potassium phosphate, 100% D2O | 100% D2O
NMR sample composition 2 mM [U-99% 15N] DHFR, 2 mM NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 100 mM potassium chloride, 50 mM potassium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 4 mM DHFR, 4 mM NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 100 mM potassium chloride, 50 mM potassium phosphate, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-99% 15N] DHFR, 1 mM NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 100 mM potassium chloride, 50 mM potassium phosphate, 5 v/v n-octylpenta-ethylene glycol (C8E5), 1.5 v/v n-octanol, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
3DFR CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE Deposited 1982-06-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 MTX METHOTREXATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DYR_LACCA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–162； UniProt 2–163

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 2l28

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2l28
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2l28
Deposition date deposition_date2010-08-13
Structure title titleSolution structure of lactobacillus casei dihydrofolate reductase apo-form, 25 conformers
Keywords keywordsOXIDOREDUCTASE, DHFR, antifolates, co-operative binding; OXIDOREDUCTASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.54 Å
Radius of gyration Rg (electron density) rg_electron15.92 Å
Forward intensity I(0) i02828360000.00
Molecular weight molecular_weight457570.0 kDa
Excluded volume excluded_volume573380 ų
Envelope volume envelope_volume40144 ų
Hydration-shell volume shell_volume18913 ų
Envelope diameter envelope_diameter57.5 Å
Shell Rg shell_rg24.03 Å
Envelope Rg envelope_rg17.67 Å
Shape Rg shape_rg15.91 Å
Total Rg total_rg16.04 Å
Total atoms total_atoms64100
Residues n_residues4050
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 dmax50.8 Å
Rg (real space) rg_real16.43 Å
Rg uncertainty (real space) rg_real_error0.23 Å
I(0) (real space) i0_real2.8280e+09
I(0) uncertainty (real space) i0_real_error3.1710e+07
Rg (reciprocal space) rg_reciprocal16.45 Å
I(0) (reciprocal space) i0_reciprocal2828000000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.4 Å
Skewness Skewness skewness0.131
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha602100.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.962
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2l28a_
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.71.1.1 — Dihydrofolate reductases

CATH v4.4 (1 domains)

Domain ID domain_id2l28A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily10 — Dihydrofolate Reductase, subunit A
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8. Citations (1)

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9. Files and Curves (10)