SAXSdb — 1dfi

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

ENOYL ACYL CARRIER PROTEIN 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–261 Chain B； UniProt 1–261 Chain C； UniProt 1–261 Chain D； UniProt 1–261	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；12% PEG 400, PH 5.0 ACETATE, 10MM NAD	Resolution 2.09 Å

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 1DFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C14 CRYSTAL STRUCTURE OF E COLI ENOYL REDUCTASE-NAD+-TRICLOSAN COMPLEX Deposited 1999-07-20	Different construct 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 1–262（262 aa） Chain B 1–262（262 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 TCL TRICLOSAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；300 K；(NH4)2SO4, PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 2.00 Å R-free 0.263
1D8A E. COLI ENOYL REDUCTASE/NAD+/TRICLOSAN COMPLEX Deposited 1999-10-21	Different construct 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 2–262（261 aa） Chain B 2–262（261 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 TCL TRICLOSAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOUR DIFFUSION；pH 7.5；290 K；PEG 400, NA HEPES, AMMONIUM SULPHATE, pH 7.5, VAPOUR DIFFUSION, temperature 290K	Resolution 2.20 Å R-free 0.294
1DFG X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD AND BENZO-DIAZABORINE Deposited 1997-01-16	Different construct 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 1–261（261 aa） Chain B 1–261（261 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NDT 2-(TOLUENE-4-SULFONYL)-2H-BENZO[D][1,2,3]DIAZABORININ-1-OL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 400, PH5.0 100MM ACETATE, 5MM NAD, 5MM 1,2-DIHYDRO-1-HYDROXY-2- (4-METHYLSULPHONYL)BENZO[E][1,2,3]DIAZABORINE	Resolution 2.50 Å
1DFH X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD AND THIENO-DIAZABORINE Deposited 1997-01-16	Different construct 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 1–261（261 aa） Chain B 1–261（261 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 TDB 6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；15% PEG 400, PH5.0 100MM ACETATE, 5MM NAD, 5MM 1,2-DIHYDRO-1-HYDROXY-2-(PROP-1-YLSULPHONYL)(5- METHYLTHIENO)[3,2-E][1,2,3]DIAZABORINE	Resolution 2.20 Å
1I2Z E. COLI ENOYL REDUCTASE IN COMPLEX WITH NAD AND BRL-12654 Deposited 2001-02-12	Different construct 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 0–261（262 aa） Chain B 0–261（262 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 654 4-(2-THIENYL)-1-(4-METHYLBENZYL)-1H-IMIDAZOLE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.273
1I30 E. Coli Enoyl Reductase +NAD+SB385826 Deposited 2001-02-12	Different construct 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 0–261（262 aa） Chain B 0–261（262 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 826 1,3,4,9-TETRAHYDRO-2-(HYDROXYBENZOYL)-9-[(4-HYDROXYPHENYL)METHYL]-6-METHOXY-2H-PYRIDO[3,4-B]INDOLE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.277
1LX6 Crystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Benzamide Inhibitor Deposited 2002-06-04	Different construct 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 0–261（262 aa） Chain B 0–261（262 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ZAM 3-[(ACETYL-METHYL-AMINO)-METHYL]-4-AMINO-N-METHYL-N-(1-METHYL-1H-INDOL-2-YLMETHYL)-BENZAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1M HEPES, 2M(NH4)2SO4,5% PEG400, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.250
1LXC Crystal Structure of E. Coli Enoyl Reductase-NAD+ with a Bound Acrylamide Inhibitor Deposited 2002-06-05	Different construct 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 0–261（262 aa） Chain B 0–261（262 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 AYM 3-(6-AMINOPYRIDIN-3-YL)-N-METHYL-N-[(1-METHYL-1H-INDOL-2-YL)METHYL]ACRYLAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES, 2M(NH4)2SO4,5% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.40 Å R-free 0.253
1MFP E. coli Enoyl Reductase in complex with NAD and SB611113 Deposited 2002-08-13	Different construct 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 0–261（262 aa） Chain B 0–261（262 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 IDN (E)-N-METHYL-N-(1-METHYL-1H-INDOL-3-YLMETHYL)-3-(7-OXO-5,6,7,8-TETRAHYDRO-[1,8]NAPHTHYRIDIN-3-YL)-ACRYLAMIDE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；NAD+, HEPES, ammonium sulfate, PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K	Resolution 2.33 Å R-free 0.259
1QG6 CRYSTAL STRUCTURE OF E. COLI ENOYL ACYL CARRIER PROTEIN REDUCTASE IN COMPLEX WITH NAD AND TRICLOSAN Deposited 1999-04-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–261（261 aa） Chain B 1–261（261 aa） Chain C 1–261（261 aa） Chain D 1–261（261 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 TCL TRICLOSAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；HANGING DROPS WERE FORMED BY MIXING 4MICROLITRES OF COMPLEX SOLUTION (15MG/ML PROTEIN, 3MM NADH, 0.6MM TRICLOSAN) WITH 4 MICROLITRES OF A RESERVOIR SOLUTION CONTAINING 12-16% (W/V) PEG 400 AND 0.1M SODIUM ACETATE PH 4.8-5.2 AT ROOM TEMPERATURE, pH 5.0	Resolution 1.90 Å R-free 0.207
1QSG CRYSTAL STRUCTURE OF ENOYL REDUCTASE INHIBITION BY TRICLOSAN Deposited 1999-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–262（262 aa） Chain B 1–262（262 aa） Chain C 1–262（262 aa） Chain D 1–262（262 aa）	Not recorded	GLC alpha-D-glucopyranose × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 TCL TRICLOSAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295.15 K；PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 1.75 Å R-free 0.215
1QSG CRYSTAL STRUCTURE OF ENOYL REDUCTASE INHIBITION BY TRICLOSAN Deposited 1999-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–262（262 aa） Chain F 1–262（262 aa） Chain G 1–262（262 aa） Chain H 1–262（262 aa）	Not recorded	GLC alpha-D-glucopyranose × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 TCL TRICLOSAN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295.15 K；PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K	Resolution 1.75 Å R-free 0.215

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FABI_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–261； UniProt 1–261 Author chain B； PDBConstruct 1–261； UniProt 1–261 Author chain C； PDBConstruct 1–261； UniProt 1–261 Author chain D； PDBConstruct 1–261； UniProt 1–261

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	1dfi
Deposition date deposition_date	1997-01-16
Structure title title	X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD
Keywords keywords	OXIDOREDUCTASE, LIPID BIOSYNTHESIS; 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	29.13 Å
Radius of gyration Rg (electron density) rg_electron	28.28 Å
Forward intensity I(0) i0	189932000.00
Molecular weight molecular_weight	107260.0 kDa
Excluded volume excluded_volume	133120 Å³
Envelope volume envelope_volume	154360 Å³
Hydration-shell volume shell_volume	43779 Å³
Envelope diameter envelope_diameter	94.0 Å
Shell Rg shell_rg	37.11 Å
Envelope Rg envelope_rg	28.34 Å
Shape Rg shape_rg	28.28 Å
Total Rg total_rg	28.98 Å
Total atoms total_atoms	7512
Residues n_residues	988
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	97.6 Å
Rg (real space) rg_real	28.99 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.8990e+08
I(0) uncertainty (real space) i0_real_error	2.7170e+06
Rg (reciprocal space) rg_reciprocal	29.05 Å
I(0) (reciprocal space) i0_reciprocal	189900000.0000
Solution quality estimate total_estimate	0.8015
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.2 Å
Skewness Skewness skewness	0.206
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	72590000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ENOYL ACYL CARRIER PROTEIN REDUCTASE
Molecular weight formula_weight	27761.7 kDa
EC 编号 ec_number	1.3.1.9
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7839

GFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNELELK

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 BL21

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	327

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dfia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d1dfib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d1dfic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d1dfid_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (4 domains)

Domain ID domain_id	1dfiA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dfiB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dfiC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1dfiD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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8. Citations (2)

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Unit-cell length a length_a	74.000 Å
Unit-cell length b length_b	81.200 Å
Unit-cell length c length_c	79.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1620
R_free r_free	—

fit	/app/data/saxs_computation/df/1dfi/1dfi.fit
pddf	/app/data/pr_computation/df/1dfi/1dfi.pr.out
profile	/app/data/saxs_computation/df/1dfi/1dfi.dat

X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD

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

ENOYL ACYL CARRIER PROTEIN 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