SAXSdb — 9xph

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

PHIKZ101

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 × 13 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain A； UniProt 1–460 Chain B； UniProt 1–460 Chain C； UniProt 1–460	Not recorded	PHIKZ174 × 6 （Q8SCY8） PHIKZ164 × 3 （Q8SCZ8） PHIKZ163.1 × 1 （L7T0L4）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8SD61_BPDPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 1–460 Author chain B； PDBConstruct 1–460； UniProt 1–460 Author chain C； PDBConstruct 1–460； UniProt 1–460

PHIKZ174

OrganismNot specified

UniProt Q8SCY8

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 × 13 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain D； UniProt 1–354 Chain E； UniProt 1–354 Chain F； UniProt 1–354 Chain G； UniProt 1–354 Chain J； UniProt 1–354 Chain L； UniProt 1–354	Not recorded	PHIKZ101 × 3 （Q8SD61） PHIKZ164 × 3 （Q8SCZ8） PHIKZ163.1 × 1 （L7T0L4）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8SCY8_BPDPK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–354； UniProt 1–354 Author chain E； PDBConstruct 1–354； UniProt 1–354 Author chain F； PDBConstruct 1–354； UniProt 1–354 Author chain G； PDBConstruct 1–354； UniProt 1–354 Author chain J； PDBConstruct 1–354； UniProt 1–354 Author chain L； PDBConstruct 1–354； UniProt 1–354

PHIKZ164

OrganismNot specified

UniProt Q8SCZ8

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 × 13 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain I； UniProt 1–293 Chain K； UniProt 1–293 Chain M； UniProt 1–293	Not recorded	PHIKZ101 × 3 （Q8SD61） PHIKZ174 × 6 （Q8SCY8） PHIKZ163.1 × 1 （L7T0L4）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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 9XPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ORJ Central spike of phiKZ phage tail Deposited 2019-04-30	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 1–293（293 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 15 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；4 M sodium chloride, 100 mM CHES, pH 9.0, 0.3% w/v sorbitol or adonitol	Resolution 2.37 Å R-free 0.206
6P20 Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164 Deposited 2019-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 262–293（32 aa） Chain B 262–293（32 aa） Chain C 262–293（32 aa）	Not recorded	MG MAGNESIUM ION × 3 STE STEARIC ACID × 1 ELA Elaidic acid × 1 EDO 1,2-ETHANEDIOL × 1 PLM PALMITIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；20-30% PEG 3350 100 mM MES ph 6.5 200-350 mM Mg(NO3)2	Resolution 1.75 Å R-free 0.191

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8SCZ8_BPDPK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–293； UniProt 1–293 Author chain K； PDBConstruct 1–293； UniProt 1–293 Author chain M； PDBConstruct 1–293； UniProt 1–293

PHIKZ163.1

OrganismNot specified

UniProt L7T0L4

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 × 13 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain H； UniProt 1–88	Not recorded	PHIKZ101 × 3 （Q8SD61） PHIKZ174 × 6 （Q8SCY8） PHIKZ164 × 3 （Q8SCZ8）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.02 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 9XPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6P1Z Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain Deposited 2019-05-20	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 D 1–88（88 aa）	Not recorded	MG MAGNESIUM ION × 1 PLM PALMITIC ACID × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；47.5-50 % PEG5500 MME 100 mM Glycine pH 10 25-100 mM KBr	Resolution 2.10 Å R-free 0.251
6P1Z Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain Deposited 2019-05-20	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 H 1–88（88 aa）	Not recorded	MG MAGNESIUM ION × 1 PLM PALMITIC ACID × 1 STE STEARIC ACID × 1 ELA Elaidic acid × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；47.5-50 % PEG5500 MME 100 mM Glycine pH 10 25-100 mM KBr	Resolution 2.10 Å R-free 0.251
6P20 Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164 Deposited 2019-05-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–88（88 aa）	Not recorded	MG MAGNESIUM ION × 3 STE STEARIC ACID × 1 ELA Elaidic acid × 1 EDO 1,2-ETHANEDIOL × 1 PLM PALMITIC ACID × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；20-30% PEG 3350 100 mM MES ph 6.5 200-350 mM Mg(NO3)2	Resolution 1.75 Å R-free 0.191

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	L7T0L4_BPDPK
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–88； UniProt 1–88

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	9xph
Deposition date deposition_date	2025-11-16
Structure title title	The structure of baseplate central region of phage phikz
Keywords keywords	spike, 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	62.85 Å
Radius of gyration Rg (electron density) rg_electron	63.04 Å
Forward intensity I(0) i0	3012010000.00
Molecular weight molecular_weight	464390.0 kDa
Excluded volume excluded_volume	581940 Å³
Envelope volume envelope_volume	1004300 Å³
Hydration-shell volume shell_volume	131450 Å³
Envelope diameter envelope_diameter	216.6 Å
Shell Rg shell_rg	64.87 Å
Envelope Rg envelope_rg	61.91 Å
Shape Rg shape_rg	63.04 Å
Total Rg total_rg	63.10 Å
Total atoms total_atoms	32732
Residues n_residues	4170
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	212.1 Å
Rg (real space) rg_real	62.77 Å
Rg uncertainty (real space) rg_real_error	2.37 Å
I(0) (real space) i0_real	3.0120e+09
I(0) uncertainty (real space) i0_real_error	6.0770e+07
Rg (reciprocal space) rg_reciprocal	62.88 Å
I(0) (reciprocal space) i0_reciprocal	3012000000.0000
Solution quality estimate total_estimate	0.6400
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.9 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.519
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	325400000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.819

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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	PHIKZ101
Molecular weight formula_weight	52013.4 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C
Atom count atom_count	32732

MAVDASSLMREVDTIINSANNYSAYKIEAKILVGDFDWVVPLRVDYFDTFRNYADGSYGDLILTELLIGTGDFQFDILPRRDELRCDVKFIPLLPNSSLLDTSRKASVKRYRCFVVLSPEDDITLTNKQSQLTSKEAMNQISYKPYRFQLVEESVYQSLMITIGKNFTNVTTADVLRAFLKQSISQLTEADDNRVIDINMEPGWNTEVRPVIPIPDGTPLKDLPNILQNKEGGVYATGLGRYIQGSYLYVYSLYDTKKYQKGAKTLNIINVPNDRLYGVEKTYVNGDTYTTILATGDASSLDKALYEMVDNGSGYRFADANKLLDDFTISKDNKMLVDAASNLYEVRGDGLKTGFQNIQWTKQRSTSNPFKHYTELAKRQGQFLKIQWNHGDADILTPGMPVKFQTVDNNVVKTYYGVLLGVDEQFAAGDNNPNPHRYVCVVTLAIFLNRSDQNEIEPST

Entity 2 Entity 2 polymer

Description description	PHIKZ174
Molecular weight formula_weight	39125.9 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,D,J,E,L,F

MVDFALPSFIGTGKDEVAKIDAYTEVSSDVRNSLVSGISNFEQGFSGILNRTLKAVRGIGDLIPSDGINLADASRRIQGALKGSRSDLQNIAQSLENIIFGELTGSNGGPGYVQQATRMANEVKMIINGVDVYKQNSNYQNMSSILSFLEDMSGSNAIIKFFDLGAEAAVLRGVLQEVAQWGIPDLIDDTFGATKRYDGSGNWVGYDYKYNDDFRFTLTKRTADSLGNNIDLDVIDRIITHSGAEALTADVPDYPNRIIANYVFPEGTKPEDYPTILSKLVSIMDKLKPDWFWTLRNTQKVFNFGVLQTASDDATTLFLSNDTYRTPMLVAPFYKPAQALELFRDMYPMIAIPT

Entity 3 Entity 3 polymer

Description description	PHIKZ164
Molecular weight formula_weight	32434.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K,M

MDEAVSLLSNMQDSEIQTSEFRLWSIGRATENKPRNSFTLMVLPIESATATDGETTFNPVEEVVDGVDADGRAYTTKVSVSRDIPCIWLPNEDNRATPPDVMRGEKIAIYRLGDTSQFYWRSMGLSNDLRTLESVVYTFNASLSPGGAGKNFDTCYFMQFSAHDKHVTIGTSKANGEPYRYSVQINTGTGAVYILDDIGNRFELVSKDKRLMLMNADNSFVKVEKKAIDLNADQYIKLTSGGSTLELNPTEFKVNTTNTTIKSSGTHIQEAGGTMTHKAGGNMLFTAPRYDFT

Entity 4 Entity 4 polymer

Description description	PHIKZ163.1
Molecular weight formula_weight	8809.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MPGIAVCNMDSAGGVILPGPNVKCFYKGQPFAVIGCAVAGHGRTPHDSARMIQGSVKMAIAGIPVCLQGSMASCGHTATGRPNLTCGS

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8. Citations (1)

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Resolution resolution	4.020 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.02 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	27796

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

The structure of baseplate central region of phage phikz

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

PHIKZ101

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ174

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ164

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ163.1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)