SAXSdb — 9yg7

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–117 Chain B； UniProt 2–117 Chain C； UniProt 2–117 Chain D； UniProt 2–117	Mutation：H24I, C51S, C71S	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CYN CYANIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1 mM Protein 10 mM KCN 0.1 M Bis-Tris pH 6.5 27% PEG MME 2000	Resolution 1.60 Å R-free 0.201

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 9YG7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7TT9 Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y34F variant Deposited 2022-02-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–117（116 aa） Chain B 2–117（116 aa） Chain C 2–117（116 aa） Chain D 2–117（116 aa）	Mutation：C51S, C71S, Y34F Mutation：C51S, C71S, Y34F Mutation：C51S, C71S, Y34F Mutation：C51S, C71S, Y34F	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M Bis-Tris, pH 6.5, 28% w/v PEG2000 MME	Resolution 2.00 Å R-free 0.203
8TLS Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y108A variant Deposited 2023-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–117（116 aa）	Mutation：C51S, C71S, Y108A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；27% PEG MME 2000, 100 mM Bis-Tris pH 5.1, 10 mM KCN, Excluded from light	Resolution 1.70 Å R-free 0.214
8TLS Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y108A variant Deposited 2023-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–117（116 aa）	Mutation：C51S, C71S, Y108A	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 CYN CYANIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；27% PEG MME 2000, 100 mM Bis-Tris pH 5.1, 10 mM KCN, Excluded from light	Resolution 1.70 Å R-free 0.214
8UGZ Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant Deposited 2023-10-06	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–117（116 aa） Chain B 2–117（116 aa） Chain C 2–117（116 aa） Chain D 2–117（116 aa）	Mutation：C51S, C71S Mutation：C51S, C71S Mutation：C51S, C71S Mutation：C51S, C71S	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CYN CYANIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；23% PEG MME 2000, 100mM Bis-Tris pH 5.5, 10mM KCN, Excluded from light	Resolution 1.80 Å R-free 0.210
8UZU Crystal structure of Shewanella benthica Group 1 truncated hemoglobin L80A C51S C71S variant Deposited 2023-11-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–117（116 aa） Chain B 2–117（116 aa） Chain C 2–117（116 aa） Chain D 2–117（116 aa）	Mutation：C51S, C71S, L80A Mutation：C51S, C71S, L80A Mutation：C51S, C71S, L80A Mutation：C51S, C71S, L80A	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CYN CYANIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；23% PEG MME 2000, 100 mM Bis-Tris pH 5.1, 10 mM KCN	Resolution 1.90 Å R-free 0.224
8VIJ Crystal structure of Shewanella benthica Group 1 truncated hemoglobin Y34F C51S C71S variant (cyanomet) Deposited 2024-01-04	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–117（116 aa） Chain B 2–117（116 aa） Chain C 2–117（116 aa） Chain D 2–117（116 aa）	Mutation：Y34F, C51S, C71S Mutation：Y34F, C51S, C71S Mutation：Y34F, C51S, C71S Mutation：Y34F, C51S, C71S	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CYN CYANIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 100 mM Bis-Tris pH 6.5, 10 mM KCN	Resolution 1.35 Å R-free 0.201
8VSH Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D Deposited 2024-01-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–117（116 aa） Chain B 2–117（116 aa） Chain C 2–117（116 aa） Chain D 2–117（116 aa）	Mutation：C51S, C71S Mutation：C51S, C71S Mutation：C51S, C71S Mutation：C51S, C71S	A1ADT {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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 5.5, 25% PEG MME 2000, 10 mM KCN, 18 days in the dark, 43 days exposed to laboratory ambient light	Resolution 2.00 Å R-free 0.226
8W3A Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S variant with trans heme D Deposited 2024-02-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–117（116 aa） Chain B 2–117（116 aa） Chain C 2–117（116 aa） Chain D 2–117（116 aa）	Mutation：C51S, C71S Mutation：C51S, C71S Mutation：C51S, C71S Mutation：C51S, C71S	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 A1ADT {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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris pH 5.5, 25% PEG MME 2000, 10 mM KCN, 18 days in the dark, 43 days exposed to laboratory ambient light	Resolution 1.80 Å R-free 0.236

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

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	9yg7
Deposition date deposition_date	2025-09-28
最后修订 last_revision	2025-10-08
Structure title title	Crystal structure of Shewanella benthica group 1 truncated hemoglobin H24I/C51S/ C71S variant
Keywords keywords	TRUNCATED HEMOGLOBIN, HEME BINDING PROTEIN, PSYCHROPIEZOPHILE, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	26.55 Å
Radius of gyration Rg (electron density) rg_electron	25.36 Å
Forward intensity I(0) i0	49070300.00
Molecular weight molecular_weight	53740.0 kDa
Excluded volume excluded_volume	66935 Å³
Envelope volume envelope_volume	79672 Å³
Hydration-shell volume shell_volume	26216 Å³
Envelope diameter envelope_diameter	83.7 Å
Shell Rg shell_rg	32.53 Å
Envelope Rg envelope_rg	25.42 Å
Shape Rg shape_rg	25.37 Å
Total Rg total_rg	26.14 Å
Total atoms total_atoms	3764
Residues n_residues	464
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	82.3 Å
Rg (real space) rg_real	26.49 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	4.9070e+07
I(0) uncertainty (real space) i0_real_error	6.8150e+05
Rg (reciprocal space) rg_reciprocal	26.51 Å
I(0) (reciprocal space) i0_reciprocal	49070000.0000
Solution quality estimate total_estimate	0.9090
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.234
Kurtosis Kurtosis kurtosis	-0.531
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14050000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.964

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Group 1 truncated hemoglobin
Molecular weight formula_weight	12813.4 kDa
Mutation mutation	H24I, 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	4607

SLYERLGGEQKIARIAADIFDTIATNPTVASRYKDSDRERVIKMVTEFLSAGTGGPQDYTGKSMPEAHRSMNINEAEYLAVIDDIMVALDKNEVGDQEKQELLMIAYSLKGEIIGA

来源 Source

来源生物 organism	Shewanella benthica KT99
NCBI Class编号 ncbi_taxonomy_id	314608
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	355

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8. Citations (1)

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Unit-cell length a length_a	27.593 Å
Unit-cell length b length_b	104.992 Å
Unit-cell length c length_c	150.977 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	orthorhombic

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	22.860 Å
R factor r_factor	0.1772
R_work r_work	0.1764
R_free r_free	0.2009

fit	/app/data/saxs_computation/yg/9yg7/9yg7.fit
pddf	/app/data/pr_computation/yg/9yg7/9yg7.pr.out
profile	/app/data/saxs_computation/yg/9yg7/9yg7.dat

Crystal structure of Shewanella benthica group 1 truncated hemoglobin H24I/C51S/ C71S variant

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction