SAXSdb — 9xpf

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

PHIKZ029

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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–695 Chain B； UniProt 1–695 Chain C； UniProt 1–695 Chain D； UniProt 1–695 Chain E； UniProt 1–695 Chain F； UniProt 1–695 Chain M； UniProt 1–695 Chain N； UniProt 1–695 Chain O； UniProt 1–695 Chain P； UniProt 1–695 Chain Q； UniProt 1–695 Chain R； UniProt 1–695	Not recorded	PHIKZ030 × 12 （Q8SDD2）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.15 Å

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 9XPF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J0H Fitting of the bacteriophage phiKZ gp29PR structure into the cryo-EM density map of the phiKZ extended tail sheath Deposited 2011-08-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane	Resolution 18.00 Å
3J0I Fitting of the phiKZ gp29PR structure into the cryo-EM density map of the phiKZ polysheath Deposited 2011-08-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane	Resolution 19.00 Å
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.286
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.286
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390) Chain B 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.286
9XPS The neck structure of the Phage Phikz Deposited 2025-11-17	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain x 1–695（695 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9XQS Structure of the inner peripheral region in the phage phiKZ baseplate complex Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain W 1–695（695 aa） Chain X 1–695（695 aa） Chain Y 1–695（695 aa） Chain Z 1–695（695 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å

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

View Construct and Data Evidence

UniProt name	Q8SDD3_BPDPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–695； UniProt 1–695 Author chain B； PDBConstruct 1–695； UniProt 1–695 Author chain C； PDBConstruct 1–695； UniProt 1–695 Author chain D； PDBConstruct 1–695； UniProt 1–695 Author chain E； PDBConstruct 1–695； UniProt 1–695 Author chain F； PDBConstruct 1–695； UniProt 1–695 Author chain M； PDBConstruct 1–695； UniProt 1–695 Author chain N； PDBConstruct 1–695； UniProt 1–695 Author chain O； PDBConstruct 1–695； UniProt 1–695 Author chain P； PDBConstruct 1–695； UniProt 1–695 Author chain Q； PDBConstruct 1–695； UniProt 1–695 Author chain R； PDBConstruct 1–695； UniProt 1–695

PHIKZ030

OrganismNot specified

UniProt Q8SDD2

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 heterocomplex Heteromer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain G； UniProt 1–293 Chain H； UniProt 1–293 Chain I； UniProt 1–293 Chain J； UniProt 1–293 Chain K； UniProt 1–293 Chain L； UniProt 1–293 Chain S； UniProt 1–293 Chain T； UniProt 1–293 Chain U； UniProt 1–293 Chain V； UniProt 1–293 Chain W； UniProt 1–293 Chain X； UniProt 1–293	Not recorded	PHIKZ029 × 12 （Q8SDD3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.15 Å

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 9XPF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XPS The neck structure of the Phage Phikz Deposited 2025-11-17	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain y 1–293（293 aa） Chain z 1–293（293 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8SDD2_BPDPK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–293； UniProt 1–293 Author chain H； PDBConstruct 1–293； UniProt 1–293 Author chain I； PDBConstruct 1–293； UniProt 1–293 Author chain J； PDBConstruct 1–293； UniProt 1–293 Author chain K； PDBConstruct 1–293； UniProt 1–293 Author chain L； PDBConstruct 1–293； UniProt 1–293 Author chain S； PDBConstruct 1–293； UniProt 1–293 Author chain T； PDBConstruct 1–293； UniProt 1–293 Author chain U； PDBConstruct 1–293； UniProt 1–293 Author chain V； PDBConstruct 1–293； UniProt 1–293 Author chain W； PDBConstruct 1–293； UniProt 1–293 Author chain X； PDBConstruct 1–293； UniProt 1–293

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	9xpf
Deposition date deposition_date	2025-11-16
Structure title title	The structure of sheath and tube proteins of phage Phikz
Keywords keywords	sheath, tube, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	85.43 Å
Radius of gyration Rg (electron density) rg_electron	85.40 Å
Forward intensity I(0) i0	22526400000.00
Molecular weight molecular_weight	1270900.0 kDa
Excluded volume excluded_volume	1585100 Å³
Envelope volume envelope_volume	2868600 Å³
Hydration-shell volume shell_volume	265840 Å³
Envelope diameter envelope_diameter	264.8 Å
Shell Rg shell_rg	95.04 Å
Envelope Rg envelope_rg	81.72 Å
Shape Rg shape_rg	85.38 Å
Total Rg total_rg	85.54 Å
Total atoms total_atoms	89568
Residues n_residues	11376
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	301.0 Å
Rg (real space) rg_real	88.96 Å
Rg uncertainty (real space) rg_real_error	1.68 Å
I(0) (real space) i0_real	2.2570e+10
I(0) uncertainty (real space) i0_real_error	4.6790e+08
Rg (reciprocal space) rg_reciprocal	86.16 Å
I(0) (reciprocal space) i0_reciprocal	22570000000.0000
Solution quality estimate total_estimate	0.8961
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	100.3 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	-0.124
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	1.0550
Highest regularization parameter α highest_alpha	21750000000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 0.880; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.562

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	PHIKZ029
Molecular weight formula_weight	77712.3 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,M,N,O,P,Q,R
Atom count atom_count	89568

MAYYNAVPRVVFNGIRDRSRRPLIRPDITFAQHCPLLRLFTETGPTETTYVGDSDDGFASIYGQASLDPRSKFFNTQSLLALNLLGRGNGFYVKRLRPEDAANPSRLIVAIEIVEDEIPLTIRRLSGFNYPNSVRDIGNAPVPTTDKVDGLKARIILIEDNTSEVGTQRVLPGTLVSDKDGSQSLVYPLFEAPVSFFGKLGDSNGMRVWSTTTADIEEFDEAAMAKFKTRQFRIQLIEKPEVGTSPVIVKTADQQDYLNITFDKGVYSDMYNADLYVGDVLVDSYSDDGVVSGLSPLYSPFSQFYVYHENIDLVRQMIYDTEMRVNPAAAAHTTAPGEIDFLTFLAVDGDPYQGIQVLGPLDGGITLGKDGNIYASGGTDGTTDLEEYAKLVDIENINFGKLNDRYNNIAEYQFGVLYDTGLPMESKYRAMRVLSARRDLQYFFTTFVETDSRLPDEATELSRVQQIITRLKAFPESTLYGTGVCRAMIVMQSGKLMDGTYRKYVPQLLDVAMSWARYAGAGTGNLVPGMEMDVSPNNRVTFVKDLNVKFFDDRVRAQAWANGATWSQSYDHRSSYYPCLRSVMLDDTSVLLSPITVNICCVLIRLIHKVHAQFSGNATLTPEQLVERCDEYILDLVRDMFGTRVNIIPRTEITPIDANNGTSWTCNVTVEANNPRTTLNFNLETVRIETPPAQQ

Entity 2 Entity 2 polymer

Description description	PHIKZ030
Molecular weight formula_weight	32686.6 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L,S,T,U,V,W,X

MARYNDPMAPETGYGAGGARNTVNLAQAGTNVFRPDLANLATNTPYVARNLVPFLLDAPRFFKYASNTNWLVACLKAFVETHTRTIDGLQRTLTVDNAEAPWGGSGEVIQTATNVTRARSNPNFGCWELQNRAIQRFLQWWINYGIADENTKVPRIVSDGIVPVEKYDATFYGMTVLFVEPDPTFQDCVNAYLCTNMFPLTTGPWENRKDASQIGQNLDLNVEFSALTDVSEGVQEYARQMFRKLNIRGMNPNNQKLDWGGLSADVLRARNGIQDQIERAVGNRVTYDGVGLS

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8. Citations (1)

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Resolution resolution	3.150 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.15 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	26028

fit	/app/data/saxs_computation/xp/9xpf/9xpf.fit
pddf	/app/data/pr_computation/xp/9xpf/9xpf.pr.out
profile	/app/data/saxs_computation/xp/9xpf/9xpf.dat

The structure of sheath and tube proteins of phage Phikz

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

PHIKZ029

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ030

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

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)