SAXSdb — 9xqd

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

PHIKZ026

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 × 23 PDB declaration: 23-meric（23） Consistent with protein copy count	Chain a； UniProt 1–552 Chain b； UniProt 1–552 Chain c； UniProt 1–552 Chain d； UniProt 1–552 Chain e； UniProt 1–552 Chain f； UniProt 1–552	Not recorded	PHIKZ027 × 2 （Q8SDD5） PHIKZ127 × 1 （Q8SD35） PHIKZ130 × 2 （Q8SD32） PHIKZ139 × 6 （Q8SD23） PHIKZ157 × 6 （Q8SD05）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.53 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	Q8SDD6_BPDPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain a； PDBConstruct 1–552； UniProt 1–552 Author chain b； PDBConstruct 1–552； UniProt 1–552 Author chain c； PDBConstruct 1–552； UniProt 1–552 Author chain d； PDBConstruct 1–552； UniProt 1–552 Author chain e； PDBConstruct 1–552； UniProt 1–552 Author chain f； PDBConstruct 1–552； UniProt 1–552

PHIKZ027

OrganismNot specified

UniProt Q8SDD5

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 × 23 PDB declaration: 23-meric（23） Consistent with protein copy count	Chain G； UniProt 1–898 Chain K； UniProt 1–898	Not recorded	PHIKZ026 × 6 （Q8SDD6） PHIKZ127 × 1 （Q8SD35） PHIKZ130 × 2 （Q8SD32） PHIKZ139 × 6 （Q8SD23） PHIKZ157 × 6 （Q8SD05）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.53 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	Q8SDD5_BPDPK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–898； UniProt 1–898 Author chain K； PDBConstruct 1–898； UniProt 1–898

PHIKZ127

OrganismNot specified

UniProt Q8SD35

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 × 23 PDB declaration: 23-meric（23） Consistent with protein copy count	Chain 0； UniProt 1–290	Not recorded	PHIKZ026 × 6 （Q8SDD6） PHIKZ027 × 2 （Q8SDD5） PHIKZ130 × 2 （Q8SD32） PHIKZ139 × 6 （Q8SD23） PHIKZ157 × 6 （Q8SD05）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.53 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	Q8SD35_BPDPK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 0； PDBConstruct 1–290； UniProt 1–290

PHIKZ130

OrganismNot specified

UniProt Q8SD32

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 × 23 PDB declaration: 23-meric（23） Consistent with protein copy count	Chain H； UniProt 1–427 Chain L； UniProt 1–427	Not recorded	PHIKZ026 × 6 （Q8SDD6） PHIKZ027 × 2 （Q8SDD5） PHIKZ127 × 1 （Q8SD35） PHIKZ139 × 6 （Q8SD23） PHIKZ157 × 6 （Q8SD05）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.53 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	Q8SD32_BPDPK
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–427； UniProt 1–427 Author chain L； PDBConstruct 1–427； UniProt 1–427

PHIKZ139

OrganismNot specified

UniProt Q8SD23

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 × 23 PDB declaration: 23-meric（23） Consistent with protein copy count	Chain 1； UniProt 1–298 Chain 2； UniProt 1–298 Chain 3； UniProt 1–298 Chain 4； UniProt 1–298 Chain 5； UniProt 1–298 Chain 6； UniProt 1–298	Not recorded	PHIKZ026 × 6 （Q8SDD6） PHIKZ027 × 2 （Q8SDD5） PHIKZ127 × 1 （Q8SD35） PHIKZ130 × 2 （Q8SD32） PHIKZ157 × 6 （Q8SD05）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.53 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 9XQD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9XPG The structure of gp139 protein of phage phikz Deposited 2025-11-16	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–298（298 aa） Chain B 1–298（298 aa） Chain C 1–298（298 aa） Chain D 1–298（298 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å

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

View Construct and Data Evidence

UniProt name	Q8SD23_BPDPK
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 1； PDBConstruct 1–298； UniProt 1–298 Author chain 2； PDBConstruct 1–298； UniProt 1–298 Author chain 3； PDBConstruct 1–298； UniProt 1–298 Author chain 4； PDBConstruct 1–298； UniProt 1–298 Author chain 5； PDBConstruct 1–298； UniProt 1–298 Author chain 6； PDBConstruct 1–298； UniProt 1–298

PHIKZ157

OrganismNot specified

UniProt Q8SD05

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 × 23 PDB declaration: 23-meric（23） Consistent with protein copy count	Chain J； UniProt 1–445 Chain N； UniProt 1–445 Chain P； UniProt 1–445 Chain R； UniProt 1–445 Chain T； UniProt 1–445 Chain V； UniProt 1–445	Not recorded	PHIKZ026 × 6 （Q8SDD6） PHIKZ027 × 2 （Q8SDD5） PHIKZ127 × 1 （Q8SD35） PHIKZ130 × 2 （Q8SD32） PHIKZ139 × 6 （Q8SD23）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.53 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	Q8SD05_BPDPK
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain J； PDBConstruct 1–445； UniProt 1–445 Author chain N； PDBConstruct 1–445； UniProt 1–445 Author chain P； PDBConstruct 1–445； UniProt 1–445 Author chain R； PDBConstruct 1–445； UniProt 1–445 Author chain T； PDBConstruct 1–445； UniProt 1–445 Author chain V； PDBConstruct 1–445； UniProt 1–445

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	9xqd
Deposition date deposition_date	2025-11-18
Structure title title	The structure of outer peripheral region in the phage phiKZ baseplate complex
Keywords keywords	baseplate, outer peripheral, 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	98.46 Å
Radius of gyration Rg (electron density) rg_electron	98.62 Å
Forward intensity I(0) i0	13629500000.00
Molecular weight molecular_weight	1007300.0 kDa
Excluded volume excluded_volume	1264000 Å³
Envelope volume envelope_volume	2460500 Å³
Hydration-shell volume shell_volume	216840 Å³
Envelope diameter envelope_diameter	336.2 Å
Shell Rg shell_rg	87.33 Å
Envelope Rg envelope_rg	93.45 Å
Shape Rg shape_rg	98.61 Å
Total Rg total_rg	98.56 Å
Total atoms total_atoms	71157
Residues n_residues	8852
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	262.3 Å
Rg (real space) rg_real	94.66 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.3060e+10
I(0) uncertainty (real space) i0_real_error	2.6290e+08
Rg (reciprocal space) rg_reciprocal	97.51 Å
I(0) (reciprocal space) i0_reciprocal	13580000000.0000
Solution quality estimate total_estimate	0.9149
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	114.8 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.513
Angular range angular_range	— – 0.0800 Å⁻¹
Current regularization parameter α current_alpha	0.8945
Highest regularization parameter α highest_alpha	403000000.0000
Real-space data points n_real_points	17
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 1.000; Stabil: 0.969; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.001

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PHIKZ026
Molecular weight formula_weight	62047.6 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c,d,e,f
Atom count atom_count	71157

MTTSYESSQYQPPQHKNHFWFRGDIVSYAGETGKAIPAKGDLVFDAAQGWFIVREVDETTGVSILDPWYMPQKPGNENEQNLLVAVGPGYSSESYRLFLDQSVTPFNICPDRRLHFYGSMVHGYKVFLGSDISEIHGKVISLFYDNAGNYLGPTIPVESVPDPLTQQNVVKALMNGRTAEKMQNGERVTLVAYDDVGGPVSIAQLVVMNTEVIAQEDTSKKYVGGITIESPFISPADPKVIEFPLNVPVESLPMMGAVHYRDGKKHVMNIDGTAMAIYGLRNYIATEEGQEFKLTLSYQLAQDELSYLSTPSANRRIQETYTARTTPVQGAYSCRMFVYPAWVNEAVGYRLEFWLANIDRQQIWNITPYVELGANSAPFNPRGYGTIQTLTYAVNLNQVDGRFLPVRFASTFQVALLSAGNNRNANWEIYSRPDQGEAYGRDLKADIEFINGNLWDLRLANGAQSQAAWLKKMYFAAEPLTGPMEATPPTPTHFRVRTVHNEYEYTVSQWNTALRINAQDMADGALLQITWIRREYDTDLQLAITALPCLQR

Entity 2 Entity 2 polymer

Description description	PHIKZ027
Molecular weight formula_weight	105364.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,K

MNAYLLRHAIDNVWCNPAQDRQFVYELKQLTPRYGVRVNWVVDYTRYKLPVQSTRDYWHLYQIGKMIPKHLGLPKVYNKWMSLNELAQNHLNLADVYVNSGINYSRNDTYVLITSSQNLLIAVKIDPLFPDLDENQPYLHVYNNAYFQSNRSDVAGHRWLVSESYRVKTISELTQFQIKIMDTIASKGGVPKYFVNGRYVNEISPVTATVGDVCDFILDPSIKRMVDFDLRTLPVFMSEIDSERKYILHYTDKTVQTIEFFDDVEAYIYQPLGNNRYTGVNYHHNESRWMRMLTHKDYSIPTARIDQFKALHPEDPRRGADPTRWPSQNWKALDNLVFRIYIHHSGYDRPLVADSHRIQILYRLKSEDIIRAMTGADSGNPLWRAENLEQSPYCWFMSAPSSFVYPLTFNLPEETSPSKVEAQNMAGDVFGYYEAANIQGYNPAWVYNDAGLKTADLRYNYWLDATVFEYDEKGILLGYNYHTAGRKYFPKDSRCAYVECINGKGSVDLHEAYGNDPVPLRDGDNWRVYVSPVWAGVPTGEWQDITDHPDRNNWGFYDDTTDDKRWVWIAKSNEWYGLVRTDEYFYLKELKFNKTDGIIKWSIRNTETHNGVKVDKLMEIPFGQYDVFVNGRPIIEGLDYTREWPQTVLCNLEYLNADPNAVNTILLRGTGFPTPDLKPYEPGEIGFIEYGVLSNDGIYKVHSNKQSRIIIDGHYRDPADLEFQEDQGTTVITDERNGAPFQIQTPQARFRDVYNDDYQARIKDDARDKQVTDFMTEYFPMKPQPNPDKIDYRYQVLSAFSCKIIHDIVKEYIKPPYQNGRYSDDDIVKQLKDYEWLAAYDIINKGYNKNKVVVYPHWYTEPVELDIFQWEYLNRILSIYLREVPPLSLFVKIKRNQP

Entity 3 Entity 3 polymer

Description description	PHIKZ127
Molecular weight formula_weight	33643.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0

MFITRDYCKVDPWTAIVEMINNNYMYQLTPGTCKLLEFEAIDHKRTRIKIDPCRDNKPGELLPVVERTEFFYQRLDFNEFFKVPQVVEVKDVYLPFTTLDLAKLICEKNDIKFDLDDFYHQEINSYNQDVTITCNPDSLRFVGEFKIKLINTVRQDISLLTKVNSFPTIVKWPAGNGNKPTAEFITMSLDFTDYRSFLLPIKAFKENPYSLEMAAILKKVTGLDFVAKSNATDYNITNIVRNGVNNFIVDYNGPVVPAYSLRNDITNVMVLRLSKTMCPNINGRLLIHYN

Entity 4 Entity 4 polymer

Description description	PHIKZ130
Molecular weight formula_weight	48651.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,H

MYTLVRSRHRIDRKSGRWTDVDLANEKISTLSVKFGDIYLYIEYPGPTAPILNALHWVNVTNEISSANPDLTVQEWLTSLGDKSLPFDDELPNEKVRLVKYAQAWHAGYIAQPVARNGHVTDGGSKFKKEDILLTHPKHKPEDVCRKCLITVNTMFHLADYTSAGVRIIDGNKTVRTANDNQIGLYSFETIGDIKYVPIKTDMIYPQQVGAPLFDATYIDMPEDIDLTNKTILLSLGGYLCVLGKGFNRVGVRTWRVDFGSLSMFDRYMQSRELIDLSSLGLEIDDKNKTLLSVEQIKKDSVIKAYMTLSQTFFIVLDSPSLFQEFVPLEPLKLPGRYQATNTRTEVYPKYTKPDQLPVVGAHGKMLDYHFIHEDKHSVYCCTLNIRNNFDAHTHDWKTEKVVDGGRYPAWPFVHDTAYLRILGVDG

Entity 5 Entity 5 polymer

Description description	PHIKZ139
Molecular weight formula_weight	32691.9 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3,4,5,6

MSAIDQQYINVTRTAYGSYLQTCKYLGIPFKLIPNTTLNEKFSIQQNVAPSAGQIPNVQYMVIGNRGHYFVKGPDGSDEVENNIHRANDAALYNHIPFVLREVADDLPAQRRNMYRLRRLEEHNGKQYFAYYARKIDVTGVVPKLLKITIVDGEPVVTPYVPNRDDLNPTPPTISNQGTVVGSNESISASAIVTVNLTAEEILEITTAHRIRTGSVRSPIISEIGLCSGVDKDVQGQSGASGNFIYTEVIACQINVFIATNHAVGYNSDGLKLTFDIGGVEPMLGSKAINVAKFVPKD

Entity 6 Entity 6 polymer

Description description	PHIKZ157
Molecular weight formula_weight	51155.7 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,P,T,V,N,R

MYNLKGFYEYPSLIDNATDKVAKFGEISDNSATYAKDKKILTSESTPSTAFIAFHSVRDEIPVDITAEYQLQVLKIGEFLLKQGNSGTIGKNTTPTQVNQMLMTEFNGKLSTVRSGPIGNMNTRLYLPEYIEFSLIVTGNEPNLIRVWLADDAFAGQYDEFKIEVVHPIGKNAQGNYDDWFKDPLEVKKLLDKFDLPTKLEEVQAKRAQYPYTYQNAYRFDYHNPRDDTMQFPAYWIVIIYGVAGNNLDIIKDAICDELLDGSAHTREEWEKILPELFRTTEFIICPFWNQLALENSDFRGGIYSPIIDPRKRIALMRRTARGSGYTTTYFDSHYELSCNIYRSVGFSVIGNAKNRNNLTQFSQVFPDYIIATNTSEDINRISVETREFLLVFADLLKAAEDMDRYTTVPMGMSRMIRDDVIYAAKVYKNINYMVVTRKSVEQFG

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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	—

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

Resolution resolution	4.530 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.53 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	131125

fit	/app/data/saxs_computation/xq/9xqd/9xqd.fit
pddf	/app/data/pr_computation/xq/9xqd/9xqd.pr.out
profile	/app/data/saxs_computation/xq/9xqd/9xqd.dat

The structure of outer peripheral region in the phage phiKZ baseplate complex

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

PHIKZ026

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ027

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ127

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ130

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ139

State in the Current Structure

Other States of the Same Protein in the Database

PHIKZ157

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (6)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)