8gog

Structure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))

Method: X-RAY DIFFRACTION

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

Streptavidin

Streptomyces avidinii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	RHODIUM(III) ION × 8 ;trichloro((3~{a}~{S},4~{S},6~{a}~{R})-4-[(5~{R})-5-oxidanyl-5-[2-(2,3,4,5-tetramethylcyclopenta-2,4-dien-1-ylidene)ethylamino]pentyl]-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-2-one)rhodium(3+) ; × 4 GLYCEROL × 18 CHLORIDE ION × 8 SULFATE ION × 10 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAV_STRAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–121； UniProt 39–157 Author chain B； PDBConstruct 3–121； UniProt 39–157

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	8gog
Deposition date deposition_date	2022-08-24
Structure title title	Structure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))
Keywords keywords	Streptavidin, Biotin, Rhodium, Enantioselectivity, Protein Engineering, Enzyme, 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.

8gog__assembly_1__model_1

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

Download this curve (.dat)

8gog__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8gog__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.92 Å
Rg (electron density)	21.69 Å
Total Rg	22.69 Å
Atom count	3930
Residues	484
Excluded volume	68708 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8gog__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 (7)

Entity 1 Entity 1 polymer

Description description	Streptavidin
Molecular weight formula_weight	12857.8 kDa
Mutation mutation	S112Y,K121E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2064

DQAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTYGTTEANAWESTLVGHDTFTKV

Source Source

Source organism organism	Streptomyces avidinii
NCBI taxonomy ID ncbi_taxonomy_id	1895
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	RHODIUM(III) ION
Molecular weight formula_weight	102.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	;trichloro((3~{a}~{S},4~{S},6~{a}~{R})-4-[(5~{R})-5-oxidanyl-5-[2-(2,3,4,5-tetramethylcyclopenta-2,4-dien-1-ylidene)ethylamino]pentyl]-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-2-one)rhodium(3+) ;
Molecular weight formula_weight	599.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	nat
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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Unit-cell length a length_a	79.450 Å
Unit-cell length b length_b	81.390 Å
Unit-cell length c length_c	90.250 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	39.730 Å
R factor r_factor	0.2532
R_work r_work	0.2510
R_free r_free	0.2942

Structure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))

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

Streptavidin

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

8gog__assembly_1__model_1

8gog__assembly_1__model_1 | I(q)

8gog__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 non-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)

Structure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))

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

Streptavidin

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

8gog__assembly_1__model_1

8gog__assembly_1__model_1 | I(q)

8gog__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 non-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)