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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–366 Chain B； UniProt 1–366	Not recorded	P7 peptide × 2 CA CALCIUM ION × 1 1PE PENTAETHYLENE GLYCOL × 9 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；MES 50mM pH 6, CaCl2 50mM, PEG400 28%+ Hampton Research PEG Ion kit B3 (1 microliter): 0.2M lithium nitrate, 20% PEG 3350 pH 7.1	Resolution 1.63 Å R-free 0.219

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6FVM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5X06 DNA replication regulation protein Deposited 2017-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa） Chain C 1–366（366 aa） Chain D 1–366（366 aa）	Not recorded	GOL GLYCEROL × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1M Tris-Cl pH 7.0, 10.5% PEG 400, 0.2M Calcium chloride, 10mM Trimethylamine-HCl, 1mM ADP, 5mM Magnesium chloride	Resolution 3.24 Å R-free 0.265
9OYB Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 1 with flexibly bound DNA at the shoulder Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9OYC Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 2 with flexibly bound DNA at the shoulder Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9OYD Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 1 conformer 3 with disordered DNA at the shoulder Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9OYE Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 1 with sharply bent DNA Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å
9OYF Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped DNA in state 2 conformer 2 with less bent DNA Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
9OYH Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 1 the DNA recognition state Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
9OYI Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 1 with fully open clamp and unsettled DNA Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
9OYJ Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 2 with fully open clamp and settled DNA Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.53 Å
9OYK Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 3 with partially closed clamp Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9OYL Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 4 with fully closed clamp Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
9OYM Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 5 with fully closed clamp Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9OYN Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped DNA in state 2 conformer 6 with fully closed clamp Deposited 2025-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.87 Å
Radius of gyration Rg (electron density) rg_electron	31.76 Å
Forward intensity I(0) i0	107716000.00
Molecular weight molecular_weight	82991.0 kDa
Excluded volume excluded_volume	104330 Å³
Envelope volume envelope_volume	140420 Å³
Hydration-shell volume shell_volume	35945 Å³
Envelope diameter envelope_diameter	97.4 Å
Shell Rg shell_rg	40.17 Å
Envelope Rg envelope_rg	30.37 Å
Shape Rg shape_rg	31.78 Å
Total Rg total_rg	32.44 Å
Total atoms total_atoms	5817
Residues n_residues	743
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	96.9 Å
Rg (real space) rg_real	32.67 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.0770e+08
I(0) uncertainty (real space) i0_real_error	1.5070e+06
Rg (reciprocal space) rg_reciprocal	32.76 Å
I(0) (reciprocal space) i0_reciprocal	107700000.0000
Solution quality estimate total_estimate	0.9011
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	50.5 Å
Skewness Skewness skewness	-0.020
Kurtosis Kurtosis kurtosis	-0.838
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	117400000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.912

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Escherichia coli O157:H7
NCBI Class编号 ncbi_taxonomy_id	83334
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/fv/6fvm/6fvm.fit
pddf	/app/data/pr_computation/fv/6fvm/6fvm.pr.out
profile	/app/data/saxs_computation/fv/6fvm/6fvm.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 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

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)