5h8y

Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal

Method: X-RAY DIFFRACTION

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

Sulfite reductase [ferredoxin], chloroplastic

Zea mays

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-1, chloroplastic × 1 （P27787） IRON/SULFUR CLUSTER × 2 SIROHEME × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 FE2/S2 (INORGANIC) CLUSTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-1, chloroplastic × 1 （P27787） IRON/SULFUR CLUSTER × 2 SIROHEME × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 FE2/S2 (INORGANIC) CLUSTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–583； UniProt 53–635 Author chain B； PDBConstruct 1–583； UniProt 53–635 Author chain C； PDBConstruct 1–583； UniProt 53–635 Author chain D； PDBConstruct 1–583； UniProt 53–635

Ferredoxin-1, chloroplastic

Zea mays

UniProt P27787

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Sulfite reductase [ferredoxin], chloroplastic × 2 （O23813） IRON/SULFUR CLUSTER × 2 SIROHEME × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 FE2/S2 (INORGANIC) CLUSTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Sulfite reductase [ferredoxin], chloroplastic × 2 （O23813） IRON/SULFUR CLUSTER × 2 SIROHEME × 2 MAGNESIUM ION × 2 CHLORIDE ION × 2 FE2/S2 (INORGANIC) CLUSTER × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FER1_MAIZE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–98； UniProt 53–150 Author chain F； PDBConstruct 1–98； UniProt 53–150

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	5h8y
Deposition date deposition_date	2015-12-25
Structure title title	Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal
Keywords keywords	ferredoxin, sulfite reductase, OXIDOREDUCTASE-ELECTRON TRANSPORT complex; OXIDOREDUCTASE/ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5h8y__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5h8y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h8y__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.12 Å
Rg (electron density)	33.78 Å
Total Rg	34.13 Å
Atom count	9699
Residues	1217
Excluded volume	172780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h8y__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5h8y__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Sulfite reductase [ferredoxin], chloroplastic
Molecular weight formula_weight	65077.9 kDa
EC 编号 ec_number	1.8.7.1
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	19620

APAKKDASEVKRSKVEIIKEKSNFLRYPLNEELVSEAPNINESAVQLIKFHGSYQQTDRDVRGQKNYSFMLRTKNPCGKVPNQLYLAMDTLADEFGIGTLRLTTRQTFQLHGVLKKNLKTVLSTVIKNMGSTLGACGDLNRNVLAPAAPYVKKDILFAQQTAENIAALLTPQSGAYYDLWVDGEKIMSAEEPPEVTKARNDNSHGTNFPDSPEPIYGTQYLPRKFKVAVTAAGDNSVDILTNDIGVVVVSDDAGEPIGFNIYVGGGMGRTHRVETTFPRLADPLGYVPKEDILYAIKAIVVTQRENGRRDDRKYSRMKYMIDRWGIDRFRAEVEKYYGKKFESFRPLPEWQFNSYLGWQEQGDGKLFYGVHVDNGRVGGQAKKTLREIIEKYNLDVSITPNQNLILCGIDQAWREPITTALAQAGLLEPKDVDPLNLTAMACPALPLCPLAQTEAERGILPILKRIRAVFNKVGIKDSESVVVRITGCPNGCARPYMAELGFVGDGPKSYQIWLGGTPNQSTLAESFMDKVKLDDIEKVLEPLFTYWNGTRQEGESFGSFTNRTGFDKLKEVVNKWAESPSAA

Source Source

Source organism organism	Zea mays
Common name common_name	Maize
NCBI taxonomy ID ncbi_taxonomy_id	4577
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ferredoxin-1, chloroplastic
Molecular weight formula_weight	10518.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA

Source Source

Source organism organism	Zea mays
Common name common_name	Maize
NCBI taxonomy ID ncbi_taxonomy_id	4577
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SIROHEME
Molecular weight formula_weight	916.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	392

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5h8ye_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

Domain ID domain_id	d5h8yf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.4 — 2Fe-2S ferredoxin-like
Family Family family	d.15.4.1 — 2Fe-2S ferredoxin-related

CATH v4.4 (9 domains)

Domain ID domain_id	5h8yA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

Domain ID domain_id	5h8yE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	30 — Beta-grasp domain

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Unit-cell length a length_a	176.219 Å
Unit-cell length b length_b	176.219 Å
Unit-cell length c length_c	195.315 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.070 Å
R factor r_factor	0.2193
R_work r_work	0.2179
R_free r_free	0.2468

Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal

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

Sulfite reductase [ferredoxin], chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Ferredoxin-1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h8y__assembly_1__model_1

5h8y__assembly_1__model_1 | I(q)

5h8y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (2 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal

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

Sulfite reductase [ferredoxin], chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ferredoxin-1, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5h8y__assembly_1__model_1

5h8y__assembly_1__model_1 | I(q)

5h8y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (2 domains)

CATH v4.4 (9 domains)

7. Citations (1)