SAXSdb — 4dvd

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

Polarity suppression protein

Enterobacteria phage P4

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–190	Mutation：C13S,C117S,T123C	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；7.5%(w/v) PEG 6000, 5%(v/v) glycerol, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.273

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 4DVD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3RX6 Crystal structure of Polarity Suppression protein from Enterobacteria phage P4 Deposited 2011-05-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa）	Not recorded	HG MERCURY (II) ION × 2 IOD IODIDE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；7.5% PEG 6000, 5% glycerol, 0.5mM DTT, 300mM NaCl, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.04 Å R-free 0.219
8PEU Rho-ATPgS-Psu complex III Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain a 1–190（190 aa） Chain b 1–190（190 aa） Chain c 1–190（190 aa） Chain d 1–190（190 aa） Chain e 1–190（190 aa） Chain f 1–190（190 aa） Chain g 1–190（190 aa） Chain h 1–190（190 aa） Chain i 1–190（190 aa） Chain j 1–190（190 aa） Chain k 1–190（190 aa） Chain l 1–190（190 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 10 MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.70 Å
8PEW Rho-ATPgS-Psu complex III expanded Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain a 1–190（190 aa） Chain b 1–190（190 aa） Chain c 1–190（190 aa） Chain d 1–190（190 aa） Chain e 1–190（190 aa） Chain f 1–190（190 aa） Chain g 1–190（190 aa） Chain h 1–190（190 aa） Chain i 1–190（190 aa） Chain j 1–190（190 aa） Chain k 1–190（190 aa） Chain l 1–190（190 aa） Chain m 1–190（190 aa） Chain n 1–190（190 aa） Chain o 1–190（190 aa） Chain p 1–190（190 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 16 MG MAGNESIUM ION × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.30 Å
8PEX Rho P167L-ATPgS-Psu complex II Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain a 1–190（190 aa） Chain b 1–190（190 aa） Chain c 1–190（190 aa） Chain d 1–190（190 aa） Chain e 1–190（190 aa） Chain f 1–190（190 aa） Chain g 1–190（190 aa） Chain h 1–190（190 aa） Chain i 1–190（190 aa） Chain j 1–190（190 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å
8PEY Rho P167L-ATPgS-Psu complex II locked Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain a 1–190（190 aa） Chain b 1–190（190 aa） Chain c 1–190（190 aa） Chain d 1–190（190 aa） Chain e 1–190（190 aa） Chain f 1–190（190 aa） Chain g 1–190（190 aa） Chain h 1–190（190 aa） Chain i 1–190（190 aa） Chain j 1–190（190 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
9GCS Rho-ATP-Psu complex II Deposited 2024-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain c 1–190（190 aa） Chain d 1–190（190 aa） Chain e 1–190（190 aa） Chain f 1–190（190 aa） Chain g 1–190（190 aa） Chain h 1–190（190 aa） Chain i 1–190（190 aa） Chain j 1–190（190 aa） Chain k 1–190（190 aa） Chain l 1–190（190 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9GCT Rho-ATP-Psu complex II expanded Deposited 2024-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain a 1–190（190 aa） Chain b 1–190（190 aa） Chain c 1–190（190 aa） Chain d 1–190（190 aa） Chain e 1–190（190 aa） Chain f 1–190（190 aa） Chain g 1–190（190 aa） Chain h 1–190（190 aa） Chain i 1–190（190 aa） Chain j 1–190（190 aa） Chain k 1–190（190 aa） Chain l 1–190（190 aa） Chain o 1–190（190 aa） Chain p 1–190（190 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 15 MG MAGNESIUM ION × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPSU_BPP4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–190； UniProt 1–190

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	4dvd
Deposition date deposition_date	2012-02-23
Structure title title	Crystal structure of the disulphide linked knotted homodimer of Psu
Keywords keywords	;All alpha protein, transcription termination inhibitor, Rho binding, capsid decoration protein of bacteriophage P4, Transcription terminator Rho helicase, TRANSCRIPTION REGULATOR ;; TRANSCRIPTION REGULATOR
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	25.17 Å
Radius of gyration Rg (electron density) rg_electron	25.03 Å
Forward intensity I(0) i0	8787330.00
Molecular weight molecular_weight	20991.0 kDa
Excluded volume excluded_volume	25912 Å³
Envelope volume envelope_volume	38447 Å³
Hydration-shell volume shell_volume	14828 Å³
Envelope diameter envelope_diameter	93.5 Å
Shell Rg shell_rg	28.52 Å
Envelope Rg envelope_rg	24.92 Å
Shape Rg shape_rg	24.98 Å
Total Rg total_rg	25.70 Å
Total atoms total_atoms	1477
Residues n_residues	187
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	92.2 Å
Rg (real space) rg_real	25.49 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	8.7870e+06
I(0) uncertainty (real space) i0_real_error	1.3190e+05
Rg (reciprocal space) rg_reciprocal	25.39 Å
I(0) (reciprocal space) i0_reciprocal	8787000.0000
Solution quality estimate total_estimate	0.7776
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.566
Kurtosis Kurtosis kurtosis	-0.293
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	658000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.625; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.238; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4dvdA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1090 — Phage polarity suppression protein monomer

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8. Citations (1)

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Unit-cell length a length_a	149.610 Å
Unit-cell length b length_b	149.610 Å
Unit-cell length c length_c	62.700 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	47.311 Å
R factor r_factor	0.2330
R_work r_work	0.2310
R_free r_free	0.2725

Description description	Polarity suppression protein
Molecular weight formula_weight	21363.0 kDa
Mutation mutation	C13S,C117S,T123C
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1480

Crystal structure of the disulphide linked knotted homodimer of Psu

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

Polarity suppression 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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Enterobacteria phage P4
NCBI Class编号 ncbi_taxonomy_id	10680
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/dv/4dvd/4dvd.fit
pddf	/app/data/pr_computation/dv/4dvd/4dvd.pr.out
profile	/app/data/saxs_computation/dv/4dvd/4dvd.dat