SAXSdb — 1vd0

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

Head decoration protein

Enterobacteria phage lambda

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 2–110	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；298 K；Pressure AMBIENT NMR sample composition：1.3mm 15N labelled GPD, 20mm sodium phosphate \| 90% H2O/10% D2O NMR sample composition：1.3mm GPD, 50mm sodium phosphate \| 100% D2O	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 1VD0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C5E BACTERIOPHAGE LAMBDA HEAD PROTEIN D Deposited 1999-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 16–110（95 aa） Chain B 16–110（95 aa） Chain C 16–110（95 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；28% PEG 4000, 0.1 M BIS-TRIS PH 6.5, 10 % GLYCEROL	Resolution 1.10 Å R-free 0.133
1TCZ Crystal structure of a truncated version of the phage lamda protein gpD Deposited 2004-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 16–110（95 aa） Fragment：N-terminal truncation Chain B 16–110（95 aa） Fragment：N-terminal truncation Chain C 16–110（95 aa） Fragment：N-terminal truncation	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.232
1TCZ Crystal structure of a truncated version of the phage lamda protein gpD Deposited 2004-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 16–110（95 aa） Fragment：N-terminal truncation Chain E 16–110（95 aa） Fragment：N-terminal truncation Chain F 16–110（95 aa） Fragment：N-terminal truncation	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.232
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
5MFD Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 Deposited 2016-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 21–110（90 aa） Fragment：UNP residues 21-110	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5	Resolution 2.30 Å R-free 0.214
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 840 PDB declaration: 840-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 70 PDB declaration: 70-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VII cryoEM structure of bacteriophage lambda capsid at 5.6 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.60 Å
7VIK Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom Deposited 2021-09-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 1–110（110 aa） Chain I 1–110（110 aa） Chain J 1–110（110 aa） Chain K 1–110（110 aa） Chain L 1–110（110 aa） Chain M 1–110（110 aa） Chain N 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.76 Å
8XQB Mature virion portal vertex of bacteriophage lambda Deposited 2024-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 71 PDB declaration: 71-meric	Chain H0 1–110（110 aa） Chain H1 1–110（110 aa） Chain H2 1–110（110 aa） Chain H3 1–110（110 aa） Chain H4 1–110（110 aa） Chain I0 1–110（110 aa） Chain I1 1–110（110 aa） Chain I2 1–110（110 aa） Chain I3 1–110（110 aa） Chain I4 1–110（110 aa） Chain J0 1–110（110 aa） Chain J1 1–110（110 aa） Chain J2 1–110（110 aa） Chain J3 1–110（110 aa） Chain J4 1–110（110 aa） Chain N0 1–110（110 aa） Chain N1 1–110（110 aa） Chain N2 1–110（110 aa） Chain N3 1–110（110 aa） Chain N4 1–110（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.07 Å

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VCAD_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 2–110

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	1vd0
Deposition date deposition_date	2004-03-17
Structure title title	Capsid stabilizing protein GPD, NMR, 20 Structures
Keywords keywords	;Virus/Viral Protein, capsid protein, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, Scottish Structural Proteomics Facility, SSPF, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Viral protein ;; VIRAL PROTEIN
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	17.36 Å
Radius of gyration Rg (electron density) rg_electron	17.09 Å
Forward intensity I(0) i0	755203000.00
Molecular weight molecular_weight	228430.0 kDa
Excluded volume excluded_volume	284600 Å³
Envelope volume envelope_volume	80410 Å³
Hydration-shell volume shell_volume	25344 Å³
Envelope diameter envelope_diameter	89.1 Å
Shell Rg shell_rg	33.13 Å
Envelope Rg envelope_rg	29.91 Å
Shape Rg shape_rg	17.06 Å
Total Rg total_rg	17.69 Å
Total atoms total_atoms	31780
Residues n_residues	2180
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	47.3 Å
Rg (real space) rg_real	15.84 Å
Rg uncertainty (real space) rg_real_error	0.10 Å
I(0) (real space) i0_real	7.1690e+08
I(0) uncertainty (real space) i0_real_error	7.7160e+06
Rg (reciprocal space) rg_reciprocal	17.76 Å
I(0) (reciprocal space) i0_reciprocal	755200000.0000
Solution quality estimate total_estimate	0.6735
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.480
Kurtosis Kurtosis kurtosis	-0.122
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	2.3790
Highest regularization parameter α highest_alpha	311600.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.016; Oscil: 0.926; Stabil: 0.994; Sysdev: 0.000; Positv: 1.000; Valcen: 0.996; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vd0a_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.2 — Head decoration protein D (gpD, major capsid protein D)
Family Family family	b.85.2.1 — Head decoration protein D (gpD, major capsid protein D)

CATH v4.4 (1 domains)

Domain ID domain_id	1vd0A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	300 — Virus Head Decoration Protein; Chain: A,
Homologous superfamily homologous superfamily	10 — Head decoration protein D

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8. Citations (2)

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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	Head decoration protein
Molecular weight formula_weight	11451.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	31780

来源生物 organism	Enterobacteria phage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli BL21(DE3)

Capsid stabilizing protein GPD, NMR, 20 Structures

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

Head decoration 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

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/vd/1vd0/1vd0.fit
pddf	/app/data/pr_computation/vd/1vd0/1vd0.pr.out
profile	/app/data/saxs_computation/vd/1vd0/1vd0.dat