SAXSdb — 6p81

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

Ubiquitin-like protein SMT3,Beta sliding clamp

Klebsiella pneumoniae IS22

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Griselimycin × 1 CALCIUM ION × 1 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 ACETATE ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–96； UniProt 13–98

Ubiquitin-like protein SMT3,Beta sliding clamp

Klebsiella pneumoniae IS22

UniProt W1BGQ6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Griselimycin × 1 CALCIUM ION × 1 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 ACETATE ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	W1BGQ6_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 97–462； UniProt 1–366

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	6p81
Deposition date deposition_date	2019-06-06
Structure title title	Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin
Keywords keywords	;SSGCID, Beta sliding clamp, DNA polymerase III, beta subunit, griselimycin, His-Smt3 fusion, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, Transferase-Antibiotic complex ;; Transferase/Antibiotic
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.

6p81__assembly_1__model_1

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

Download this curve (.dat)

6p81__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p81__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.01 Å
Rg (electron density)	28.49 Å
Total Rg	29.01 Å
Atom count	3477
Residues	444
Excluded volume	62135 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p81__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein SMT3,Beta sliding clamp
Molecular weight formula_weight	51735.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3949

MGHHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

Source Source

Source organism organism	Klebsiella pneumoniae IS22
NCBI taxonomy ID ncbi_taxonomy_id	1432547
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Griselimycin
Molecular weight formula_weight	1115.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XVPTLPLVPXG

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
Molecular weight formula_weight	178.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	398

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6p81A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

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Unit-cell length a length_a	71.020 Å
Unit-cell length b length_b	83.100 Å
Unit-cell length c length_c	188.180 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	47.014 Å
R factor r_factor	0.1858
R_work r_work	0.1848
R_free r_free	0.2126

Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin

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

Ubiquitin-like protein SMT3,Beta sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,Beta sliding clamp

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

6p81__assembly_1__model_1

6p81__assembly_1__model_1 | I(q)

6p81__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 polymer

Polymer 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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin

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

Ubiquitin-like protein SMT3,Beta sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,Beta sliding clamp

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

6p81__assembly_1__model_1

6p81__assembly_1__model_1 | I(q)

6p81__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 polymer

Polymer 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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)