6nl7

Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)

Method: X-RAY DIFFRACTION

▼

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

Immunoglobulin G-binding protein G

Streptococcus

UniProt P19909

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ACETATE ION × 2 SODIUM ION × 2 CHLORIDE ION × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ACETATE ION × 3 SODIUM ION × 1 PHOSPHATE ION × 1 DIPHOSPHATE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ACETATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPG2_STRSG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–56； UniProt 303–357 Author chain B； PDBConstruct 2–56； UniProt 303–357 Author chain C； PDBConstruct 2–56； UniProt 303–357 Author chain D； PDBConstruct 2–56； UniProt 303–357

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nl7
Deposition date deposition_date	2019-01-08
Structure title title	Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)
Keywords keywords	Metal-mediated complex, B1 Domain of Streptococcal protein G, Immunoglobulin binding protein, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6nl7__assembly_1__model_1

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

Download this curve (.dat)

6nl7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nl7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	12.41 Å
Rg (electron density)	11.00 Å
Total Rg	12.70 Å
Atom count	459
Residues	56
Excluded volume	8178 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nl7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nl7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6nl7__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6nl7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Immunoglobulin G-binding protein G
Molecular weight formula_weight	6247.9 kDa
Mutation mutation	T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q
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	2325

MTYKLILNGKTLKGEFTAEAHDAAHAEYIFRALAKAQGVDGEWTYDDATKTFTVTE

Source Source

Source organism organism	Streptococcus
NCBI taxonomy ID ncbi_taxonomy_id	1301
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

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	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	DIPHOSPHATE
Molecular weight formula_weight	173.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6nl7A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6nl7B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6nl7C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	6nl7D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	40.903 Å
Unit-cell length b length_b	63.057 Å
Unit-cell length c length_c	53.225 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	40.060 Å
R factor r_factor	0.1151
R_work r_work	0.1129
R_free r_free	0.1581

Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)

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

Immunoglobulin G-binding protein G

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

6nl7__assembly_1__model_1

6nl7__assembly_1__model_1 | I(q)

6nl7__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 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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21H, T25H, K28Y, V29I, K31R, Q32A, Y33L, N35K, D36A, N37Q)

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

Immunoglobulin G-binding protein G

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

6nl7__assembly_1__model_1

6nl7__assembly_1__model_1 | I(q)

6nl7__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 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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)