SAXSdb — 6pqk

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

Ribonuclease

Bacillus amyloliquefaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Barstar × 1 （P11540） PHOSPHATE ION × 3 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Barstar × 1 （P11540） PHOSPHATE ION × 1 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNBR_BACAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–128； UniProt 48–157 Author chain C； PDBConstruct 19–128； UniProt 48–157

Barstar

Bacillus amyloliquefaciens

UniProt P11540

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ribonuclease × 1 （P00648） PHOSPHATE ION × 3 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ribonuclease × 1 （P00648） PHOSPHATE ION × 1 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BARS_BACAM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–90； UniProt 1–90 Author chain D； PDBConstruct 1–90； UniProt 1–90

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	6pqk
Deposition date deposition_date	2019-07-09
Structure title title	Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A
Keywords keywords	disulfide, Toxin-Antitoxin, complex, nuclease, RNA BINDING PROTEIN; RNA 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.

6pqk__assembly_1__model_1

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

Download this curve (.dat)

6pqk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6pqk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.53 Å
Rg (electron density)	17.43 Å
Total Rg	18.50 Å
Atom count	1598
Residues	196
Excluded volume	28194 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6pqk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6pqk__assembly_2__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Ribonuclease
Molecular weight formula_weight	14522.1 kDa
EC 编号 ec_number	3.1.27.-
Mutation mutation	A43C, S80C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4014

MGSSHHHHHHSQDPIEGRAQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLCDVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTCGFRNSDRILYSSDWLIYKTTDHYQTFTKIR

Source Source

Source organism organism	Bacillus amyloliquefaciens
NCBI taxonomy ID ncbi_taxonomy_id	1390
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Barstar
Molecular weight formula_weight	10336.7 kDa
Mutation mutation	C40A, S59C, A67C, C82A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQCKQLTENGCESVLQVFREAKAEGADITIILS

Source Source

Source organism organism	Bacillus amyloliquefaciens
NCBI taxonomy ID ncbi_taxonomy_id	1390
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	420

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6pqka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

Domain ID domain_id	d6pqkb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.9 — Barstar-like
Superfamily Superfamily superfamily	c.9.1 — Barstar-related
Family Family family	c.9.1.1 — Barstar-related

Domain ID domain_id	d6pqkc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

Domain ID domain_id	d6pqkd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.9 — Barstar-like
Superfamily Superfamily superfamily	c.9.1 — Barstar-related
Family Family family	c.9.1.1 — Barstar-related

CATH v4.4 (4 domains)

Domain ID domain_id	6pqkA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	6pqkB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	10 — Barstar-like

Domain ID domain_id	6pqkC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	6pqkD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	370 — Barnase; Chain D
Homologous superfamily homologous superfamily	10 — Barstar-like

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Unit-cell length a length_a	36.704 Å
Unit-cell length b length_b	68.404 Å
Unit-cell length c length_c	166.723 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	35.590 Å
R factor r_factor	0.1379
R_work r_work	0.1375
R_free r_free	0.1600

Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A

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

Ribonuclease

State in the Current Structure

Other States of the Same Protein in the Database

Barstar

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

6pqk__assembly_1__model_1

6pqk__assembly_1__model_1 | I(q)

6pqk__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A

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

Ribonuclease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Barstar

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

6pqk__assembly_1__model_1

6pqk__assembly_1__model_1 | I(q)

6pqk__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)