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1ddi

CRYSTAL STRUCTURE OF SIR-FP60

Method: X-RAY DIFFRACTION Dmax: 74.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SULFITE REDUCTASE [NADPH] FLAVOPROTEIN ALPHA-COMPONENT

Escherichia coli

UniProt P38038

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 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

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 1DDI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DDG 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 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
1DDG CRYSTAL STRUCTURE OF SIR-FP60 Deposited 1999-11-10 Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 226–599（374 aa） Fragment：SIR-FP60
Not recorded 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
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 3 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

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 1ddi

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ddi
Deposition date deposition_date1999-11-10
Structure title titleCRYSTAL STRUCTURE OF SIR-FP60
Keywords keywordsCYTOCHROME P450 REDUCTASE, FNR, FLAVOPROTEIN, MODULAR PROTEIN, 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_guinier23.56 Å
Radius of gyration Rg (electron density) rg_electron22.87 Å
Forward intensity I(0) i031230700.00
Molecular weight molecular_weight42092.0 kDa
Excluded volume excluded_volume52274 ų
Envelope volume envelope_volume62840 ų
Hydration-shell volume shell_volume23179 ų
Envelope diameter envelope_diameter77.3 Å
Shell Rg shell_rg29.61 Å
Envelope Rg envelope_rg22.98 Å
Shape Rg shape_rg22.87 Å
Total Rg total_rg23.66 Å
Total atoms total_atoms2976
Residues n_residues374
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 dmax74.2 Å
Rg (real space) rg_real23.54 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real3.1230e+07
I(0) uncertainty (real space) i0_real_error3.7750e+05
Rg (reciprocal space) rg_reciprocal23.54 Å
I(0) (reciprocal space) i0_reciprocal31230000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.5 Å
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6610000.0000
Real-space data points n_real_points65
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: 0.996; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ddia1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.1 — NADPH-cytochrome p450 reductase FAD-binding domain-like
Domain ID domain_idd1ddia2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.4 — NADPH-cytochrome p450 reductase-like

CATH v4.4 (3 domains)

Domain ID domain_id1ddiA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1ddiA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id1ddiA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
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8. Citations (1)

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9. Files and Curves (10)