SAXSdb — 1ddg

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

SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 226–599	Fragment：SIR-FP60	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.01 Å R-free 0.289
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 226–599	Fragment：SIR-FP60	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.01 Å R-free 0.289

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 1DDG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DDI CRYSTAL STRUCTURE OF SIR-FP60 Deposited 1999-11-10	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 226–599（374 aa） Fragment：SIR-FP60	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 4K	Resolution 2.51 Å R-free 0.245
1YKG Solution structure of the flavodoxin-like domain from the Escherichia coli sulfite reductase Deposited 2005-01-18	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 52–218（167 aa） Fragment：SiR-FP18, flavodoxin-like domain	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer；Pressure ambient NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 100mM phosphate buffer, 2mM MgCl2；Pressure ambient NMR sample composition 1.5mM U-15N, U-13C, 80%-2H SiR-FP18 \| 100mM phosphate buffer pH 7.0, H2O/D2O 90:10 NMR sample composition 1.5mM U-15N, U-13C, SiR-FP18 \| 100mM phosphate buffer pH 7.0, H2O/D2O 90:10 NMR sample composition 1.5mM U-15N, U-13C, SiR-FP18 \| 100mM phosphate buffer pH 7.0, D2O NMR sample composition 1.5mM U-15N, SiR-FP18 \| 100mM phosphate buffer pH 7.0, H2O/D2O 90:10 NMR sample composition 1.5mM U-15N, U-13C, 80%-2H SiR-FP18 \| 100mM phosphate buffer pH 7.0, 2mM MgCl2, H2O/D2O 90:10, + 14mg/ml filamentous Pf1 phage NMR sample composition 1.5mM U-15N, U-13C, 80%-2H SiR-FP18 \| 100mM phosphate buffer pH 7.0, H2O/D2O 90:10, +5% C12E5/hexanol with r=0.96 NMR sample composition 1.5mM U-15N, SiR-FP18 \| 100mM phosphate buffer pH 7.0, D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYSJ_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–374； UniProt 226–599 Author chain B； PDBConstruct 1–374； UniProt 226–599

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	1ddg
Deposition date deposition_date	1999-11-10
Structure title title	CRYSTAL STRUCTURE OF SIR-FP60
Keywords keywords	CYTOCHROME P450 REDUCTASE, FNR, FLAVOPROTEIN, MODULAR PROTEIN, 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	57.23 Å
Radius of gyration Rg (electron density) rg_electron	57.60 Å
Forward intensity I(0) i0	108675000.00
Molecular weight molecular_weight	86192.0 kDa
Excluded volume excluded_volume	107230 Å³
Envelope volume envelope_volume	183760 Å³
Hydration-shell volume shell_volume	26447 Å³
Envelope diameter envelope_diameter	165.5 Å
Shell Rg shell_rg	64.96 Å
Envelope Rg envelope_rg	52.62 Å
Shape Rg shape_rg	57.61 Å
Total Rg total_rg	57.78 Å
Total atoms total_atoms	6087
Residues n_residues	748
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	165.9 Å
Rg (real space) rg_real	57.74 Å
Rg uncertainty (real space) rg_real_error	1.67 Å
I(0) (real space) i0_real	1.0870e+08
I(0) uncertainty (real space) i0_real_error	2.1000e+06
Rg (reciprocal space) rg_reciprocal	56.69 Å
I(0) (reciprocal space) i0_reciprocal	108500000.0000
Solution quality estimate total_estimate	0.5459
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.074
Kurtosis Kurtosis kurtosis	-1.566
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2426000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.005; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.079; Smooth: 0.000

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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	SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT
Molecular weight formula_weight	42329.5 kDa
EC 编号 ec_number	1.8.1.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6697

IHTSPYSKDAPLVASLSVNQKITGRNSEKDVRHIEIDLGDSGLRYQPGDALGVWYQNDPALVKELVELLWLKGDEPVTVEGKTLPLNEALQWHFELTVNTANIVENYATLTRSETLLPLVGDKAKLQHYAATTPIVDMVRFSPAQLDAEALINLLRPLTPRLYSIASSQAEVENEVHVTVGVVRYDVEGRARAGGASSFLADRVEEEGEVRVFIEHNDNFRLPANPETPVIMIGPGTGIAPFRAFMQQRAADEAPGKNWLFFGNPHFTEDFLYQVEWQRYVKEGVLTRIDLAWSRDQKEKVYVQDKLREQGAELWRWINDGAHIYVCGDANRMAKDVEQALLEVIAEFGGMDTEAADEFLSELRVERRYQRDVY

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	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	548

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ddga1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.1 — NADPH-cytochrome p450 reductase FAD-binding domain-like

Domain ID domain_id	d1ddga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.4 — NADPH-cytochrome p450 reductase-like

Domain ID domain_id	d1ddgb1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.1 — NADPH-cytochrome p450 reductase FAD-binding domain-like

Domain ID domain_id	d1ddgb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.4 — NADPH-cytochrome p450 reductase-like

CATH v4.4 (6 domains)

Domain ID domain_id	1ddgA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	1ddgA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

Domain ID domain_id	1ddgA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

Domain ID domain_id	1ddgB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	1ddgB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

Domain ID domain_id	1ddgB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

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8. Citations (1)

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Unit-cell length a length_a	34.840 Å
Unit-cell length b length_b	82.540 Å
Unit-cell length c length_c	105.360 Å
Unit-cell angle α angle_alpha	79.71 °
Unit-cell angle β angle_beta	83.05 °
Unit-cell angle γ angle_gamma	89.90 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	0.2890

fit	/app/data/saxs_computation/dd/1ddg/1ddg.fit
pddf	/app/data/pr_computation/dd/1ddg/1ddg.pr.out
profile	/app/data/saxs_computation/dd/1ddg/1ddg.dat

CRYSTAL STRUCTURE OF SIR-FP60

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

SULFITE REDUCTASE (NADPH) FLAVOPROTEIN ALPHA-COMPONENT

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