SAXSdb — 2dpd

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

Replication termination protein

Bacillus subtilis

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–122 Chain B； UniProt 1–122	Mutation：C110S	5'-D(CPTPAPTPGPAPAPCPAPTPAPAPTPGPTPTPCPAPTPAPG)-3' × 1 5'-D(CPTPAPTPGPAPAPCPAPTPTPAPTPGPTPTPCPAPTPAPG)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25% MPD, 75mM sodium acetate pH 4.6, 20mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.17 Å R-free 0.278

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 2DPD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BM9 REPLICATION TERMINATOR PROTEIN FROM BACILLUS SUBTILIS Deposited 1998-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.00 Å R-free 0.281
1BM9 REPLICATION TERMINATOR PROTEIN FROM BACILLUS SUBTILIS Deposited 1998-07-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–122（122 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.00 Å R-free 0.281
1F4K CRYSTAL STRUCTURE OF THE REPLICATION TERMINATOR PROTEIN/B-SITE DNA COMPLEX Deposited 2000-06-08	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：C110S Mutation：C110S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；5% PEG 4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.50 Å R-free 0.276
1J0R Crystal structure of the replication termination protein mutant C110S Deposited 2002-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa）	Mutation：C110S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；22% PEG 2000, 150mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.279
1J0R Crystal structure of the replication termination protein mutant C110S Deposited 2002-11-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–122（122 aa）	Mutation：C110S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；22% PEG 2000, 150mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.279
2DPU Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA Deposited 2006-05-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 8–129（122 aa）	Mutation：C110S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；1.75M ammonium sulfate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.306
2DQR Crystal structure of the replication terminator protein mutant RTP.E39K.R42Q Deposited 2006-05-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：E39K,R42Q Mutation：E39K,R42Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；22% PEG 4000, 0.2M sodium acetate, 0.225M Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.01 Å R-free 0.276
2DQR Crystal structure of the replication terminator protein mutant RTP.E39K.R42Q Deposited 2006-05-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–122（122 aa） Chain D 1–122（122 aa）	Mutation：E39K,R42Q Mutation：E39K,R42Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；22% PEG 4000, 0.2M sodium acetate, 0.225M Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.01 Å R-free 0.276
2EFW Crystal structure of the RTP:nRB complex from Bacillus subtilis Deposited 2007-02-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–122（122 aa） Chain B 1–122（122 aa）	Mutation：C110S Mutation：C110S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；2% PEG 4000, 125mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.332
2EFW Crystal structure of the RTP:nRB complex from Bacillus subtilis Deposited 2007-02-26	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain F 1–122（122 aa） Chain G 1–122（122 aa）	Mutation：C110S Mutation：C110S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；2% PEG 4000, 125mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.332

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RTP_BACSU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 1–122 Author chain B； PDBConstruct 1–122； UniProt 1–122

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	2dpd
Deposition date deposition_date	2006-05-09
Structure title title	Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site
Keywords keywords	winged-helix protein-DNA complex, Replication Termination, Fork Arrest Mechanism, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/DNA
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	23.47 Å
Radius of gyration Rg (electron density) rg_electron	22.92 Å
Forward intensity I(0) i0	35909200.00
Molecular weight molecular_weight	40370.0 kDa
Excluded volume excluded_volume	47985 Å³
Envelope volume envelope_volume	59116 Å³
Hydration-shell volume shell_volume	22304 Å³
Envelope diameter envelope_diameter	85.2 Å
Shell Rg shell_rg	28.92 Å
Envelope Rg envelope_rg	23.12 Å
Shape Rg shape_rg	22.88 Å
Total Rg total_rg	23.68 Å
Total atoms total_atoms	2794
Residues n_residues	274
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	80.9 Å
Rg (real space) rg_real	23.54 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	3.5910e+07
I(0) uncertainty (real space) i0_real_error	5.4470e+05
Rg (reciprocal space) rg_reciprocal	23.52 Å
I(0) (reciprocal space) i0_reciprocal	35910000.0000
Solution quality estimate total_estimate	0.7909
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.438
Kurtosis Kurtosis kurtosis	-0.223
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4177000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.928; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5'-D(CPTPAPTPGPAPAPCPAPTPAPAPTPGPTPTPCPAPTPAP*G)-3'
Molecular weight formula_weight	6445.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	2806

CTATGAACATAATGTTCATAG

Entity 2 Entity 2 polymer

Description description	5'-D(CPTPAPTPGPAPAPCPAPTPTPAPTPGPTPTPCPAPTPAP*G)-3'
Molecular weight formula_weight	6436.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CTATGAACATTATGTTCATAG

Entity 3 Entity 3 polymer

Description description	Replication termination protein
Molecular weight formula_weight	14531.1 kDa
Mutation mutation	C110S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKEEKRSSTGFLVKQRAFLKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDDGILKQIKVKKEGAKLQEVVLYQFKDYEAAKLYKKQLKVELDRSKKLIEKALSDNF

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli BL21

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dpda_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.7 — Replication terminator protein (RTP)

Domain ID domain_id	d2dpdb_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.7 — Replication terminator protein (RTP)

CATH v4.4 (2 domains)

Domain ID domain_id	2dpdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2dpdB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	117.006 Å
Unit-cell length b length_b	117.006 Å
Unit-cell length c length_c	165.553 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.170 Å
Low-resolution limit resolution_low	60.000 Å
R factor r_factor	0.2384
R_work r_work	0.2361
R_free r_free	0.2778

fit	/app/data/saxs_computation/dp/2dpd/2dpd.fit
pddf	/app/data/pr_computation/dp/2dpd/2dpd.pr.out
profile	/app/data/saxs_computation/dp/2dpd/2dpd.dat

Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site

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

Replication termination protein

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)