SAXSdb — 1b5t

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

PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)

Escherichia coli

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 21–295 Chain B； UniProt 21–295 Chain C； UniProt 21–295	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

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 1B5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 1–296（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
1ZPT Escherichia coli Methylenetetrahydrofolate Reductase (reduced) complexed with NADH, pH 7.25 Deposited 2005-05-17	Different construct 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 1–296（296 aa） Chain B 1–296（296 aa） Chain C 1–296（296 aa）	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
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 construct 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 1–275； UniProt 21–295 Author chain B； PDBConstruct 1–275； UniProt 21–295 Author chain C； PDBConstruct 1–275； UniProt 21–295

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b5t
Deposition date deposition_date	1999-01-07
Structure title title	ESCHERICHIA COLI METHYLENETETRAHYDROFOLATE REDUCTASE
Keywords keywords	BETA ALPHA BARREL, REDUCTASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	34.56 Å
Radius of gyration Rg (electron density) rg_electron	34.23 Å
Forward intensity I(0) i0	136458000.00
Molecular weight molecular_weight	91185.0 kDa
Excluded volume excluded_volume	112730 Å³
Envelope volume envelope_volume	147520 Å³
Hydration-shell volume shell_volume	36169 Å³
Envelope diameter envelope_diameter	115.3 Å
Shell Rg shell_rg	40.27 Å
Envelope Rg envelope_rg	34.01 Å
Shape Rg shape_rg	34.26 Å
Total Rg total_rg	34.58 Å
Total atoms total_atoms	6380
Residues n_residues	816
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	113.2 Å
Rg (real space) rg_real	34.57 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	1.3650e+08
I(0) uncertainty (real space) i0_real_error	2.4710e+06
Rg (reciprocal space) rg_reciprocal	34.57 Å
I(0) (reciprocal space) i0_reciprocal	136500000.0000
Solution quality estimate total_estimate	0.8865
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	110.7 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.599
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23610000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.844

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)
Molecular weight formula_weight	30782.1 kDa
EC 编号 ec_number	1.7.99.5
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6564

GQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRPA

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1b5ta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.23 — FAD-linked oxidoreductase
Family Family family	c.1.23.1 — Methylenetetrahydrofolate reductase

Domain ID domain_id	d1b5tb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.23 — FAD-linked oxidoreductase
Family Family family	c.1.23.1 — Methylenetetrahydrofolate reductase

Domain ID domain_id	d1b5tc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.23 — FAD-linked oxidoreductase
Family Family family	c.1.23.1 — Methylenetetrahydrofolate reductase

CATH v4.4 (3 domains)

Domain ID domain_id	1b5tA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	1b5tB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	1b5tC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	220 —

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8. Citations (1)

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Unit-cell length a length_a	103.000 Å
Unit-cell length b length_b	128.200 Å
Unit-cell length c length_c	98.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	121.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.2630

fit	/app/data/saxs_computation/b5/1b5t/1b5t.fit
pddf	/app/data/pr_computation/b5/1b5t/1b5t.pr.out
profile	/app/data/saxs_computation/b5/1b5t/1b5t.dat

ESCHERICHIA COLI METHYLENETETRAHYDROFOLATE REDUCTASE

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

PROTEIN (METHYLENETETRAHYDROFOLATE REDUCTASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction