SAXSdb — 1b77

▼

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

PROTEIN (SLIDING CLAMP)

Enterobacteria phage RB69

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–228 Chain B； UniProt 1–228 Chain C； UniProt 1–228	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；16-18% PEG 8000, 0.2 M CA ACETATE PH7.5	Resolution 2.10 Å R-free 0.269

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 1B77	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B8H SLIDING CLAMP, DNA POLYMERASE Deposited 1999-02-01	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–228（228 aa） Chain B 1–228（228 aa） Chain C 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 3.00 Å R-free 0.313

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPA5_BPR69
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 1–228 Author chain B； PDBConstruct 1–228； UniProt 1–228 Author chain C； PDBConstruct 1–228； UniProt 1–228

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	1b77
Deposition date deposition_date	1999-01-27
Structure title title	BUILDING A REPLISOME STRUCTURE FROM INTERACTING PIECES: A SLIDING CLAMP COMPLEXED WITH AN INTERACTION PEPTIDE FROM DNA POLYMERASE
Keywords keywords	SLIDING CLAMP, GP45, REPLISOME; SLIDING CLAMP
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.17 Å
Radius of gyration Rg (electron density) rg_electron	33.06 Å
Forward intensity I(0) i0	87014300.00
Molecular weight molecular_weight	75314.0 kDa
Excluded volume excluded_volume	94848 Å³
Envelope volume envelope_volume	132950 Å³
Hydration-shell volume shell_volume	33026 Å³
Envelope diameter envelope_diameter	98.5 Å
Shell Rg shell_rg	40.93 Å
Envelope Rg envelope_rg	31.39 Å
Shape Rg shape_rg	33.09 Å
Total Rg total_rg	33.68 Å
Total atoms total_atoms	5298
Residues n_residues	684
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

▼

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

Maximum dimension Dmax dmax	100.7 Å
Rg (real space) rg_real	34.03 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	8.7010e+07
I(0) uncertainty (real space) i0_real_error	1.3450e+06
Rg (reciprocal space) rg_reciprocal	34.12 Å
I(0) (reciprocal space) i0_reciprocal	87020000.0000
Solution quality estimate total_estimate	0.8951
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	52.5 Å
Skewness Skewness skewness	-0.039
Kurtosis Kurtosis kurtosis	-0.893
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46900000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.940

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1b77a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1b77a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1b77b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1b77b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1b77c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1b77c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

CATH v4.4 (3 domains)

Domain ID domain_id	1b77A00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1b77B00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1b77C00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	65.900 Å
Unit-cell length b length_b	87.600 Å
Unit-cell length c length_c	138.200 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	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2250
R_free r_free	0.2690

Description description	PROTEIN (SLIDING CLAMP)
Molecular weight formula_weight	25133.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6011

BUILDING A REPLISOME STRUCTURE FROM INTERACTING PIECES: A SLIDING CLAMP COMPLEXED WITH AN INTERACTION PEPTIDE FROM DNA POLYMERASE

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

PROTEIN (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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Enterobacteria phage RB69
NCBI Class编号 ncbi_taxonomy_id	12353
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	713

fit	/app/data/saxs_computation/b7/1b77/1b77.fit
pddf	/app/data/pr_computation/b7/1b77/1b77.pr.out
profile	/app/data/saxs_computation/b7/1b77/1b77.dat