1d4c

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

Method: X-RAY DIFFRACTION D_max: 173.8 Å Quality: GOOD

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

FLAVOCYTOCHROME C FUMARATE REDUCTASE

OrganismNot specified

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	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 25–596	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 25–596	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 25–596	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

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 1D4C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D4D CRYSTAL STRUCTURE OF THE SUCCINATE COMPLEXED 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 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
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 2 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 Author chain B； PDBConstruct 1–572； UniProt 25–596 Author chain C； PDBConstruct 1–572； UniProt 25–596 Author chain D； 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d4c
Deposition date deposition_date	1999-10-03
Structure title title	CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1
Keywords keywords	TETRAHEME FLAVOCYTOCHROME C, 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	54.37 Å
Radius of gyration Rg (electron density) rg_electron	54.13 Å
Forward intensity I(0) i0	925669000.00
Molecular weight molecular_weight	247140.0 kDa
Excluded volume excluded_volume	305740 Å³
Envelope volume envelope_volume	448620 Å³
Hydration-shell volume shell_volume	68168 Å³
Envelope diameter envelope_diameter	173.8 Å
Shell Rg shell_rg	60.02 Å
Envelope Rg envelope_rg	51.34 Å
Shape Rg shape_rg	54.13 Å
Total Rg total_rg	54.28 Å
Total atoms total_atoms	17344
Residues n_residues	2274
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	173.8 Å
Rg (real space) rg_real	54.27 Å
Rg uncertainty (real space) rg_real_error	1.75 Å
I(0) (real space) i0_real	9.2570e+08
I(0) uncertainty (real space) i0_real_error	2.0340e+07
Rg (reciprocal space) rg_reciprocal	54.42 Å
I(0) (reciprocal space) i0_reciprocal	925800000.0000
Solution quality estimate total_estimate	0.8622
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	77.9 Å
Skewness Skewness skewness	0.041
Kurtosis Kurtosis kurtosis	-0.786
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39330000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.690

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	FLAVOCYTOCHROME C FUMARATE REDUCTASE
Molecular weight formula_weight	59974.7 kDa
EC 编号 ec_number	1.3.99.1
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17470

AAPEVLADFHGEMGGCDSCHVSDKGGVTNDNLTHENGQCVSCHGDLKELAAAAPKDKVSPHKSHLIGEIACTSCHKGHEKSVAYCDACHSFGFDMPFGGKWERKFVPVDADKAAQDKAIAAGVKETTDVVIIGSGGAGLAAAVSARDAGAKVILLEKEPIPGGNTKLAAGGMNAAETKPQAKLGIEDKKQIMIDDTMKGGRNINDPELVKVLANNSSDSIDWLTSMGADMTDVGRMGGASVNRSHRPTGGAGVGAHVAQVLWDNAVKRGTDIRLNSRVVRILEDASGKVTGVLVKGEYTGYYVIKADAVVIAAGGFAKNNERVSKYDPKLKGFKATNHPGATGDGLDVALQAGAATRDLEYIQAHPTYSPAGGVMITEAVRGNGAIVVNREGNRFMNEITTRDKASAAILQQKGESAYLVFDDSIRKSLKAIEGYVHLNIVKEGKTIEELAKQIDVPAAELAKTVTAYNGFVKSGKDAQFERPDLPRELVVAPFYALEIAPAVHHTMGGLVIDTKAEVKSEKTGKPITGLYAAGEVTGGVHGANRLGGNAISDIVTYGRIAGASAAKFAKDN

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	16

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	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	126

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1d4ca1
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1d4ca2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d1d4ca3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	d1d4cb1
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1d4cb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d1d4cb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	d1d4cc1
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1d4cc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d1d4cc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	d1d4cd1
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

Domain ID domain_id	d1d4cd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain

Domain ID domain_id	d1d4cd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily Superfamily superfamily	d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family Family family	d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

CATH v4.4 (12 domains)

Domain ID domain_id	1d4cA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1d4cA02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1d4cA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	1d4cB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1d4cB02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1d4cB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	1d4cC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1d4cC02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1d4cC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

Domain ID domain_id	1d4cD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

Domain ID domain_id	1d4cD02
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	1d4cD03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	700 — Flavocytochrome C3; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	109.690 Å
Unit-cell length b length_b	216.360 Å
Unit-cell length c length_c	112.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2100
R_free r_free	0.3000

fit	/app/data/saxs_computation/d4/1d4c/1d4c.fit
pddf	/app/data/pr_computation/d4/1d4c/1d4c.pr.out
profile	/app/data/saxs_computation/d4/1d4c/1d4c.dat