8zxr

Crystal structure of Ssr1698 in complex with heme c

Method: X-RAY DIFFRACTION

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

Ssr1698 protein

Synechocystis sp. (strain PCC 6803 / Kazusa)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cytochrome c × 1 （P00004） NICKEL (II) ION × 1 CHLORIDE ION × 2 HEME C × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	Cytochrome c × 6 （P00004） NICKEL (II) ION × 6 CHLORIDE ION × 12 HEME C × 6 GLYCEROL × 6 water × 12	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Cytochrome c × 3 （P00004） NICKEL (II) ION × 3 CHLORIDE ION × 6 HEME C × 3 GLYCEROL × 3 water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Cytochrome c × 2 （P00004） NICKEL (II) ION × 2 CHLORIDE ION × 4 HEME C × 2 GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P73129_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–97； UniProt 1–96

Cytochrome c

OrganismNot specified

UniProt P00004

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ssr1698 protein × 1 （P73129） NICKEL (II) ION × 1 CHLORIDE ION × 2 HEME C × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	Ssr1698 protein × 6 （P73129） NICKEL (II) ION × 6 CHLORIDE ION × 12 HEME C × 6 GLYCEROL × 6 water × 12	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Ssr1698 protein × 3 （P73129） NICKEL (II) ION × 3 CHLORIDE ION × 6 HEME C × 3 GLYCEROL × 3 water × 6	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Ssr1698 protein × 2 （P73129） NICKEL (II) ION × 2 CHLORIDE ION × 4 HEME C × 2 GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYC_HORSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 12–22

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	8zxr
Deposition date deposition_date	2024-06-14
Structure title title	Crystal structure of Ssr1698 in complex with heme c
Keywords keywords	Ssr1698, heme b, heme c, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

8zxr__assembly_1__model_1

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

Download this curve (.dat)

8zxr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8zxr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.26 Å
Rg (electron density)	13.98 Å
Total Rg	15.21 Å
Atom count	848
Residues	106
Excluded volume	15085 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8zxr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8zxr__assembly_2__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8zxr__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8zxr__assembly_4__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Ssr1698 protein
Molecular weight formula_weight	11643.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1002

MMADPLTPAISDRICKHMNEDHASAIALYAQVFGQQTDVTMAQMQAIDPTGMDLVVESEGGSKTIRIEFEQPLKDSEDAHQVLIAMAKQARSVGKNSLEHHHHHH

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytochrome c
Molecular weight formula_weight	1246.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VQKCAQCHTVQ

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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Unit-cell length a length_a	83.597 Å
Unit-cell length b length_b	83.597 Å
Unit-cell length c length_c	69.300 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	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	36.200 Å
R factor r_factor	0.1873
R_work r_work	0.1857
R_free r_free	0.2177

Crystal structure of Ssr1698 in complex with heme c

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

Ssr1698 protein

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c

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

8zxr__assembly_1__model_1

8zxr__assembly_1__model_1 | I(q)

8zxr__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

7. Citations (1)

Crystal structure of Ssr1698 in complex with heme c

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

Ssr1698 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c

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

8zxr__assembly_1__model_1

8zxr__assembly_1__model_1 | I(q)

8zxr__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

7. Citations (1)