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1zpt

Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 7.25

Method: X-RAY DIFFRACTION Dmax: 111.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

5,10-methylenetetrahydrofolate reductase

Escherichia coli

UniProt P00394

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 1–296 Chain B； UniProt 1–296 Chain C； UniProt 1–296 Not recorded SO4 SULFATE ION × 5 FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K Resolution 1.95 Å R-free 0.246

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 1ZPT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B5T ESCHERICHIA COLI METHYLENETETRAHYDROFOLATE REDUCTASE Deposited 1999-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 21–295（275 aa）
Chain B 21–295（275 aa）
Chain C 21–295（275 aa）
Not recorded HG MERCURY (II) ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 2.50 Å R-free 0.263
1ZP3 E. coli Methylenetetrahydrofolate Reductase (oxidized) Deposited 2005-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–296（296 aa）
Chain C 1–296（296 aa）
Not recorded SO4 SULFATE ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 1.85 Å R-free 0.237
1ZP3 E. coli Methylenetetrahydrofolate Reductase (oxidized) Deposited 2005-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–296（296 aa）
Chain C 1–296（296 aa）
Not recorded SO4 SULFATE ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 1.85 Å R-free 0.237
1ZP3 E. coli Methylenetetrahydrofolate Reductase (oxidized) Deposited 2005-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–296（296 aa）
Not recorded SO4 SULFATE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 1.85 Å R-free 0.237
1ZP4 Glu28Gln mutant of E. coli Methylenetetrahydrofolate Reductase (oxidized) complex with Methyltetrahydrofolate Deposited 2005-05-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–296（296 aa）
Chain B 1–296（296 aa）
Chain C 1–296（296 aa）
Mutation：E28Q Mutation：E28Q Mutation：E28Q SO4 SULFATE ION × 2 C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 1.85 Å R-free 0.231
1ZRQ Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 6.0 Deposited 2005-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–296（296 aa）
Chain C 1–296（296 aa）
Not recorded SO4 SULFATE ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 6.00
Resolution 2.20 Å R-free 0.252
1ZRQ Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 6.0 Deposited 2005-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–296（296 aa）
Chain C 1–296（296 aa）
Not recorded SO4 SULFATE ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 6.00
Resolution 2.20 Å R-free 0.252
1ZRQ Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 6.0 Deposited 2005-05-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–296（296 aa）
Chain B 1–296（296 aa）
Chain C 1–296（296 aa）
Not recorded SO4 SULFATE ION × 8 FAD FLAVIN-ADENINE DINUCLEOTIDE × 6 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；295 K；PEG 4000, LITHIUM SULFATE, SODIUM CACODYLATE, ETHANOL, MESO-ERYTHRITOL, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 6.00
Resolution 2.20 Å R-free 0.252

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name METF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–296； UniProt 1–296 Author chain B； PDBConstruct 1–296； UniProt 1–296 Author chain C； PDBConstruct 1–296； UniProt 1–296

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 1zpt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1zpt
Deposition date deposition_date2005-05-17
Structure title titleEscherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 7.25
Keywords keywordsTIM BARREL, FLAVIN, REDUCTASE, NADH, OXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier34.29 Å
Radius of gyration Rg (electron density) rg_electron33.72 Å
Forward intensity I(0) i0148903000.00
Molecular weight molecular_weight94420.0 kDa
Excluded volume excluded_volume116620 ų
Envelope volume envelope_volume145100 ų
Hydration-shell volume shell_volume37389 ų
Envelope diameter envelope_diameter120.3 Å
Shell Rg shell_rg38.86 Å
Envelope Rg envelope_rg33.48 Å
Shape Rg shape_rg33.72 Å
Total Rg total_rg34.08 Å
Total atoms total_atoms6627
Residues n_residues821
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 dmax111.4 Å
Rg (real space) rg_real34.37 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real1.4890e+08
I(0) uncertainty (real space) i0_real_error2.2650e+06
Rg (reciprocal space) rg_reciprocal34.32 Å
I(0) (reciprocal space) i0_reciprocal148900000.0000
Solution quality estimate total_estimate0.8819
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.5 Å
Skewness Skewness skewness0.333
Kurtosis Kurtosis kurtosis-0.596
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha40390000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.836
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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) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1zpta_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.23 — FAD-linked oxidoreductase
Family Family familyc.1.23.1 — Methylenetetrahydrofolate reductase
Domain ID domain_idd1zptb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.23 — FAD-linked oxidoreductase
Family Family familyc.1.23.1 — Methylenetetrahydrofolate reductase
Domain ID domain_idd1zptc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.23 — FAD-linked oxidoreductase
Family Family familyc.1.23.1 — Methylenetetrahydrofolate reductase

CATH v4.4 (3 domains)

Domain ID domain_id1zptA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily220 —
Domain ID domain_id1zptB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily220 —
Domain ID domain_id1zptC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily220 —
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8. Citations (1)

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9. Files and Curves (10)