SAXSdb — 1bde

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

VPR PROTEIN

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 50–82	Fragment：VPR 50-82 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1 NMR sample composition：50% TFE-D3/50% H2O	Resolution not provided

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 1BDE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DSJ NMR SOLUTION STRUCTURE OF VPR50_75, 20 STRUCTURES Deposited 1997-10-23	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 50–75（26 aa） Fragment：RESIDUES 50 - 75	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.3；298 K	Resolution not provided
1DSK NMR SOLUTION STRUCTURE OF VPR59_86, 20 STRUCTURES Deposited 1997-10-23	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–86（28 aa） Fragment：RESIDUES 59 - 86	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.3；298 K	Resolution not provided
1KZS Structure of Human Immunodeficiency Virus Type 1 Vpr(34-51) Peptide in Aqueous TFE Solution Deposited 2002-02-08	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–51（18 aa） Fragment：RESIDUES 34-51	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2 mM Vpr(34-51); 50 % H2O, 50 % TFE \| 50 % H2O, 50 % TFE	Resolution not provided
1KZT Structure of Human Immunodeficiency Virus Type 1 Vpr(34-51) Peptide in DPC Micelle Containing Aqueous Solution Deposited 2002-02-08	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–51（18 aa） Fragment：RESIDUES 34-51	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 2mM Vpr(34-51); 100mM Dodecylphosphocholine d38; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1KZV Structure of Human Immunodeficiency Virus Type 1 Vpr(34-51) Peptide in Chloroform Methanol Deposited 2002-02-08	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–51（18 aa） Fragment：RESIDUES 34-51	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2 mM Vpr(34-51); 50 % Methanol d3, 50 % Chloroform d1 \| 50 % Methanol d3, 50 % Chloroform d1	Resolution not provided
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000	Resolution 3.49 Å R-free 0.206
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000	Resolution 3.49 Å R-free 0.206
6XQI Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09	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 × 4 PDB declaration: tetrameric	Chain A 16–78（63 aa） Chain B 16–78（63 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M Tris, pH 7.5, 10% PEG 4000	Resolution 2.34 Å R-free 0.220
6XQI Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 16–78（63 aa） Chain D 16–78（63 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M Tris, pH 7.5, 10% PEG 4000	Resolution 2.34 Å R-free 0.220
6XQJ Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–79（79 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 927 uM [U-100% 2H; U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1100 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1110 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1000 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 745 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	VPR_HV1N5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–34； UniProt 50–82

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	1bde
Deposition date deposition_date	1998-05-07
Structure title title	HELICAL STRUCTURE OF POLYPEPTIDES FROM THE C-TERMINAL HALF OF HIV-1 VPR, NMR, 20 STRUCTURES
Keywords keywords	AIDS, HIV, VIRAL PROTEIN, VPR FRAGMENT, HELIX; AIDS
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.67 Å
Radius of gyration Rg (electron density) rg_electron	14.63 Å
Forward intensity I(0) i0	79758000.00
Molecular weight molecular_weight	77692.0 kDa
Excluded volume excluded_volume	98573 Å³
Envelope volume envelope_volume	14925 Å³
Hydration-shell volume shell_volume	8056 Å³
Envelope diameter envelope_diameter	65.0 Å
Shell Rg shell_rg	21.65 Å
Envelope Rg envelope_rg	19.36 Å
Shape Rg shape_rg	14.64 Å
Total Rg total_rg	14.83 Å
Total atoms total_atoms	11120
Residues n_residues	660
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	58.9 Å
Rg (real space) rg_real	15.18 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	7.9760e+07
I(0) uncertainty (real space) i0_real_error	1.0840e+06
Rg (reciprocal space) rg_reciprocal	15.14 Å
I(0) (reciprocal space) i0_reciprocal	79760000.0000
Solution quality estimate total_estimate	0.5423
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	6.7 Å
Skewness Skewness skewness	0.614
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7625.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.015; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.001; Smooth: 0.000

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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

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bdea_
Class class	j — Peptides
Fold Fold fold	j.11 — VPR protein fragments
Superfamily Superfamily superfamily	j.11.1 — VPR protein fragments
Family Family family	j.11.1.1 — VPR protein fragments

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	VPR PROTEIN
Molecular weight formula_weight	3870.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11120

fit	/app/data/saxs_computation/bd/1bde/1bde.fit
pddf	/app/data/pr_computation/bd/1bde/1bde.pr.out
profile	/app/data/saxs_computation/bd/1bde/1bde.dat

HELICAL STRUCTURE OF POLYPEPTIDES FROM THE C-TERMINAL HALF OF HIV-1 VPR, NMR, 20 STRUCTURES

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

VPR 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)