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1d4d

CRYSTAL STRUCTURE OF THE SUCCINATE COMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1

Method: X-RAY DIFFRACTION Dmax: 82.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

FLAVOCYTOCHROME C FUMARATE REDUCTASE

OrganismNot specified

UniProt P83223

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 25–596 Not recorded HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；ammonium sulfate with added ethanol and succinate, bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K Resolution 2.50 Å R-free 0.305

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 1D4D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D4C CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 Deposited 1999-10-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–596（572 aa）
Not recorded HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Resolution 2.90 Å R-free 0.300
1D4C CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 Deposited 1999-10-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 25–596（572 aa）
Not recorded HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Resolution 2.90 Å R-free 0.300
1D4C CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 Deposited 1999-10-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 25–596（572 aa）
Not recorded HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Resolution 2.90 Å R-free 0.300
1D4C CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 Deposited 1999-10-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 25–596（572 aa）
Not recorded HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；ammonium sulfate with added PEG 400, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Resolution 2.90 Å R-free 0.300
1D4E CRYSTAL STRUCTURE OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1 COMPLEXED WITH FUMARATE Deposited 1999-10-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–596（572 aa）
Not recorded HEC HEME C × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FUM FUMARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；ammonium sulfate with ethanol and fumarate added, bicine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Resolution 2.80 Å R-free 0.311

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FRDA_SHEON
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–572； UniProt 25–596

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 1d4d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d4d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d4d
Deposition date deposition_date1999-10-03
Structure title titleCRYSTAL STRUCTURE OF THE SUCCINATE COMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1
Keywords keywordstetraheme flavocytochrome c fumarate reductase, 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_guinier24.66 Å
Radius of gyration Rg (electron density) rg_electron23.86 Å
Forward intensity I(0) i062901500.00
Molecular weight molecular_weight59753.0 kDa
Excluded volume excluded_volume73708 ų
Envelope volume envelope_volume84750 ų
Hydration-shell volume shell_volume29367 ų
Envelope diameter envelope_diameter83.3 Å
Shell Rg shell_rg31.47 Å
Envelope Rg envelope_rg24.00 Å
Shape Rg shape_rg23.87 Å
Total Rg total_rg24.61 Å
Total atoms total_atoms4198
Residues n_residues560
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 dmax82.9 Å
Rg (real space) rg_real24.58 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real6.2900e+07
I(0) uncertainty (real space) i0_real_error8.5700e+05
Rg (reciprocal space) rg_reciprocal24.60 Å
I(0) (reciprocal space) i0_reciprocal62900000.0000
Solution quality estimate total_estimate0.8824
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.9 Å
Skewness Skewness skewness0.287
Kurtosis Kurtosis kurtosis-0.381
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha16780000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.996
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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_idd1d4da1
Class classa — All alpha proteins
Fold Fold folda.138 — Multiheme cytochromes
Superfamily Superfamily superfamilya.138.1 — Multiheme cytochromes
Family Family familya.138.1.3 — Di-heme elbow motif
Domain ID domain_idd1d4da2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain
Domain ID domain_idd1d4da3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamilyd.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family familyd.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id1d4dA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Flavocytochrome C3; Chain A
Domain ID domain_id1d4dA02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1d4dA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
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8. Citations (1)

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9. Files and Curves (10)