SAXSdb — 6fvm

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

Beta sliding clamp

Escherichia coli O157:H7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	P7 peptide × 2 CALCIUM ION × 1 PENTAETHYLENE GLYCOL × 9 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3B_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–368； UniProt 1–366 Author chain B； PDBConstruct 3–368； 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	6fvm
Deposition date deposition_date	2018-03-04
Structure title title	Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
Keywords keywords	DNA sliding clamp, DNA BINDING PROTEIN; DNA 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.

6fvm__assembly_1__model_1

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

Download this curve (.dat)

6fvm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fvm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.87 Å
Rg (electron density)	31.76 Å
Total Rg	32.44 Å
Atom count	5817
Residues	744
Excluded volume	104330 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Beta sliding clamp
Molecular weight formula_weight	40865.8 kDa
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	6425

SHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSPVQIEDAASQSAAYVVMPMRL

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	P7 peptide
Molecular weight formula_weight	700.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I

XQADLF

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	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	462

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6fvmA01
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

Domain ID domain_id	6fvmB01
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	34.336 Å
Unit-cell length b length_b	78.653 Å
Unit-cell length c length_c	80.182 Å
Unit-cell angle α angle_alpha	113.26 °
Unit-cell angle β angle_beta	97.82 °
Unit-cell angle γ angle_gamma	95.97 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.631 Å
Low-resolution limit resolution_low	66.302 Å
R factor r_factor	0.1821
R_work r_work	0.1802
R_free r_free	0.2192

Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide

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

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

6fvm__assembly_1__model_1

6fvm__assembly_1__model_1 | I(q)

6fvm__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide

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

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

6fvm__assembly_1__model_1

6fvm__assembly_1__model_1 | I(q)

6fvm__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)