SAXSdb — 2dpu

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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 4 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 8–129	Mutation：C110S	5'-D(PAPTPGPTPTPCPAPTPAPG)-3' × 2 5'-D(CPTPAPTPGPAPAPCPAPTP*T)-3' × 2	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

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 2DPU	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 construct Different mutation/modification Different oligomeric state 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 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 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
2DPD Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site Deposited 2006-05-09	Different construct Different mutation/modification Different oligomeric state 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；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
2DQR Crystal structure of the replication terminator protein mutant RTP.E39K.R42Q Deposited 2006-05-29	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） 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 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 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 8–129

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	2dpu
Deposition date deposition_date	2006-05-15
Structure title title	Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA
Keywords keywords	protein-DNA complex, winged-helix, DNA replication, 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	18.28 Å
Radius of gyration Rg (electron density) rg_electron	17.56 Å
Forward intensity I(0) i0	9684960.00
Molecular weight molecular_weight	20058.0 kDa
Excluded volume excluded_volume	23861 Å³
Envelope volume envelope_volume	30146 Å³
Hydration-shell volume shell_volume	15030 Å³
Envelope diameter envelope_diameter	65.6 Å
Shell Rg shell_rg	22.91 Å
Envelope Rg envelope_rg	18.00 Å
Shape Rg shape_rg	17.51 Å
Total Rg total_rg	18.50 Å
Total atoms total_atoms	1388
Residues n_residues	135
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	68.0 Å
Rg (real space) rg_real	18.29 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	9.6850e+06
I(0) uncertainty (real space) i0_real_error	1.3980e+05
Rg (reciprocal space) rg_reciprocal	18.29 Å
I(0) (reciprocal space) i0_reciprocal	9685000.0000
Solution quality estimate total_estimate	0.8325
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	-0.045
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1241000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.998

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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(PAPTPGPTPTPCPAPTPAPG)-3'
Molecular weight formula_weight	3059.0 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	1396

ATGTTCATAG

Entity 2 Entity 2 polymer

Description description	5'-D(CPTPAPTPGPAPAPCPAPTP*T)-3'
Molecular weight formula_weight	3332.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CTATGAACATT

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2dpua_
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 (1 domains)

Domain ID domain_id	2dpuA00
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	73.049 Å
Unit-cell length b length_b	73.049 Å
Unit-cell length c length_c	68.411 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	6

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2061
R_work r_work	0.2020
R_free r_free	0.3061

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

Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)