SAXSdb — 8vsh

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

Group 1 truncated hemoglobin

Shewanella benthica KT99

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	;{3-[(2R,5'R)-9',14'-diethenyl-5'-hydroxy-5',10',15',19'-tetramethyl-5-oxo-4,5-dihydro-3H-spiro[furan-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.13,6.18,11.113,16]tetracosa[1,3(24),6,8,10,12,14,16(22),17,19]decaen]-20'-yl-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]propanoato}iron ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9DF82_9GAMM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 2–117 Author chain B； PDBConstruct 1–116； UniProt 2–117 Author chain C； PDBConstruct 1–116； UniProt 2–117 Author chain D； PDBConstruct 1–116； UniProt 2–117

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	8vsh
Deposition date deposition_date	2024-01-24
Structure title title	Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D
Keywords keywords	GLOBIN, 2/2 HEMOGLOBIN, HEME BINDING PROTEIN, PSYCHROPIEZOPHILE, HEME-BINDING PROTEIN; HEME-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.

8vsh__assembly_1__model_1

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

Download this curve (.dat)

8vsh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vsh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.45 Å
Rg (electron density)	25.34 Å
Total Rg	26.11 Å
Atom count	3768
Residues	464
Excluded volume	66833 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vsh__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Group 1 truncated hemoglobin
Molecular weight formula_weight	12838.4 kDa
Mutation mutation	C51S, C71S
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	4024

SLYERLGGEQKIARIAADIFDTHATNPTVASRYKDSDRERVIKMVTEFLSAGTGGPQDYTGKSMPEAHRSMNINEAEYLAVIDDIMVALDKNEVGDQEKQELLMIAYSLKGEIIGA

Source Source

Source organism organism	Shewanella benthica KT99
NCBI taxonomy ID ncbi_taxonomy_id	314608
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;{3-[(2R,5'R)-9',14'-diethenyl-5'-hydroxy-5',10',15',19'-tetramethyl-5-oxo-4,5-dihydro-3H-spiro[furan-2,4'-[21,22,23,24]tetraazapentacyclo[16.2.1.13,6.18,11.113,16]tetracosa[1,3(24),6,8,10,12,14,16(22),17,19]decaen]-20'-yl-kappa~4~N~21'~,N~22'~,N~23'~,N~24'~]propanoato}iron ;
Molecular weight formula_weight	632.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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Unit-cell length a length_a	27.364 Å
Unit-cell length b length_b	104.604 Å
Unit-cell length c length_c	150.710 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.030 Å
R factor r_factor	0.1930
R_work r_work	0.1907
R_free r_free	0.2260

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D

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

Group 1 truncated hemoglobin

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

8vsh__assembly_1__model_1

8vsh__assembly_1__model_1 | I(q)

8vsh__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D

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

Group 1 truncated hemoglobin

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

8vsh__assembly_1__model_1

8vsh__assembly_1__model_1 | I(q)

8vsh__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)