SAXSdb — 5jj1

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

Portal protein

Enterobacteria phage P22

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 homooligomer Homooligomer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–602 Chain B； UniProt 1–602 Chain C； UniProt 1–602 Chain D； UniProt 1–602 Chain E； UniProt 1–602 Chain F； UniProt 1–602 Chain G； UniProt 1–602 Chain H； UniProt 1–602 Chain I； UniProt 1–602 Chain J； UniProt 1–602 Chain K； UniProt 1–602 Chain L； UniProt 1–602	Fragment：UNP residues 1-602	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；5% PEG 8,000, 10 mM Cesium Chloride	Resolution 3.30 Å R-free 0.315

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 5JJ1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LJ5 Full Length Bacteriophage P22 Portal Protein Deposited 2010-01-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–725（725 aa） Fragment：UNP residues 1-725 Chain B 1–725（725 aa） Fragment：UNP residues 1-725 Chain C 1–725（725 aa） Fragment：UNP residues 1-725 Chain D 1–725（725 aa） Fragment：UNP residues 1-725 Chain E 1–725（725 aa） Fragment：UNP residues 1-725 Chain F 1–725（725 aa） Fragment：UNP residues 1-725 Chain G 1–725（725 aa） Fragment：UNP residues 1-725 Chain H 1–725（725 aa） Fragment：UNP residues 1-725 Chain I 1–725（725 aa） Fragment：UNP residues 1-725 Chain J 1–725（725 aa） Fragment：UNP residues 1-725 Chain K 1–725（725 aa） Fragment：UNP residues 1-725 Chain L 1–725（725 aa） Fragment：UNP residues 1-725	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；30% tert-Butanol, 70mM sodium chloride, 2.5% PEG 400, 0.1M sodium acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 7.50 Å R-free 0.263
4V4K Bacteriophage P22 Portal Protein bound to middle Tail Factor GP4. This file contain the second biological assembly Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain M 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain N 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain O 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain P 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain Q 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain R 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain S 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain T 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain U 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain V 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain W 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain X 1–602（602 aa） Fragment：UNP RESIDUES 1-602	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；20% PEG 8000, 0.1M (NH4)2HPO4, 0.1M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K	Resolution 3.25 Å R-free 0.236
4V4K Bacteriophage P22 Portal Protein bound to middle Tail Factor GP4. This file contain the second biological assembly Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain B 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain C 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain D 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain E 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain F 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain G 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain H 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain I 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain J 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain K 1–602（602 aa） Fragment：UNP RESIDUES 1-602 Chain L 1–602（602 aa） Fragment：UNP RESIDUES 1-602	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；20% PEG 8000, 0.1M (NH4)2HPO4, 0.1M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K	Resolution 3.25 Å R-free 0.236
5GAI Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins Deposited 2015-12-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 27 PDB declaration: 27-meric	Chain A 5–725（721 aa） Chain B 5–725（721 aa） Chain C 5–725（721 aa） Chain D 5–725（721 aa） Chain E 5–725（721 aa） Chain F 5–725（721 aa） Chain G 5–725（721 aa） Chain H 5–725（721 aa） Chain I 5–725（721 aa） Chain J 5–725（721 aa） Chain W 5–725（721 aa） Chain X 5–725（721 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2 seconds before plunging.	Resolution 10.50 Å
5JJ3 Refined Structure of the Mature Virion Conformation of P22 Portal Protein Deposited 2016-04-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–725（725 aa） Chain B 1–725（725 aa） Chain C 1–725（725 aa） Chain D 1–725（725 aa） Chain E 1–725（725 aa） Chain F 1–725（725 aa） Chain G 1–725（725 aa） Chain H 1–725（725 aa） Chain I 1–725（725 aa） Chain J 1–725（725 aa） Chain K 1–725（725 aa） Chain L 1–725（725 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；30% tert-butanol, 70 mM sodium chloride, 2.5% PEG400 in 0.1 M sodium acetate	Resolution 7.00 Å R-free 0.260
8EAO Cryo-EM structure of the in-situ gp1-gp4 complex from bacteriophage P22 Deposited 2022-08-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain B 6–626（621 aa） Chain D 6–626（621 aa） Chain F 6–626（621 aa） Chain H 6–626（621 aa） Chain J 6–626（621 aa） Chain L 6–626（621 aa） Chain N 6–626（621 aa） Chain P 6–626（621 aa） Chain R 6–626（621 aa） Chain T 6–626（621 aa） Chain V 6–626（621 aa） Chain X 6–626（621 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8TVU In situ cryo-EM structure of bacteriophage P22 portal protein: head-to-tail protein complex at 3.0A resolution Deposited 2023-08-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–725（725 aa） Chain B 1–725（725 aa） Chain D 1–725（725 aa） Chain F 1–725（725 aa） Chain H 1–725（725 aa） Chain J 1–725（725 aa） Chain L 1–725（725 aa） Chain N 1–725（725 aa） Chain P 1–725（725 aa） Chain R 1–725（725 aa） Chain T 1–725（725 aa） Chain W 1–725（725 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8U10 In situ cryo-EM structure of bacteriophage P22 gp1:gp4:gp5:gp10:gp9 N-term complex in conformation 1 at 3.2A resolution Deposited 2023-08-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 58 PDB declaration: 58-meric	Chain a 1–725（725 aa） Chain b 1–725（725 aa） Chain c 1–725（725 aa） Chain d 1–725（725 aa） Chain e 1–725（725 aa） Chain f 1–725（725 aa） Chain g 1–725（725 aa） Chain h 1–725（725 aa） Chain i 1–725（725 aa） Chain j 1–725（725 aa） Chain k 1–725（725 aa） Chain l 1–725（725 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8U11 In situ cryo-EM structure of bacteriophage P22 gp1:gp5:gp4: gp10: gp9 N-term complex in conformation 2 at 3.1A resolution Deposited 2023-08-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 58 PDB declaration: 58-meric	Chain a 1–725（725 aa） Chain b 1–725（725 aa） Chain c 1–725（725 aa） Chain d 1–725（725 aa） Chain e 1–725（725 aa） Chain f 1–725（725 aa） Chain g 1–725（725 aa） Chain h 1–725（725 aa） Chain i 1–725（725 aa） Chain j 1–725（725 aa） Chain k 1–725（725 aa） Chain l 1–725（725 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9KYW The scaffold C-loop of phage P22 Deposited 2024-12-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–725（725 aa） Chain L 1–725（725 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
9PDP In situ cryoEM structure of bacteriophage P22 portal barrel Deposited 2025-06-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: 12-meric	Chain A 602–710（109 aa） Chain B 602–710（109 aa） Chain C 602–710（109 aa） Chain D 602–710（109 aa） Chain E 602–710（109 aa） Chain F 602–710（109 aa） Chain G 602–710（109 aa） Chain H 602–710（109 aa） Chain I 602–710（109 aa） Chain J 602–710（109 aa） Chain K 602–710（109 aa） Chain L 602–710（109 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.83 Å
9PGG Cryo-EM structure of bacteriophage P22 gp1-gp5-gp4 complex at 2.76 angstrom Deposited 2025-07-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 39 PDB declaration: 39-meric	Chain Bb 1–725（725 aa） Chain Bd 1–725（725 aa） Chain Bf 1–725（725 aa） Chain Bh 1–725（725 aa） Chain Bj 1–725（725 aa） Chain Bl 1–725（725 aa） Chain Bn 1–725（725 aa） Chain Bp 1–725（725 aa） Chain Br 1–725（725 aa） Chain Bt 1–725（725 aa） Chain Bv 1–725（725 aa） Chain Bx 1–725（725 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PORTL_BPP22
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–602； UniProt 1–602 Author chain B； PDBConstruct 1–602； UniProt 1–602 Author chain C； PDBConstruct 1–602； UniProt 1–602 Author chain D； PDBConstruct 1–602； UniProt 1–602 Author chain E； PDBConstruct 1–602； UniProt 1–602 Author chain F； PDBConstruct 1–602； UniProt 1–602 Author chain G； PDBConstruct 1–602； UniProt 1–602 Author chain H； PDBConstruct 1–602； UniProt 1–602 Author chain I； PDBConstruct 1–602； UniProt 1–602 Author chain J； PDBConstruct 1–602； UniProt 1–602 Author chain K； PDBConstruct 1–602； UniProt 1–602 Author chain L； PDBConstruct 1–602； UniProt 1–602

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	5jj1
Deposition date deposition_date	2016-04-22
Structure title title	Structure of the Immature Procapsid Conformation of P22 Portal Protein
Keywords keywords	portal protein; dodecamer; packaging motor; procapsid, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	65.16 Å
Radius of gyration Rg (electron density) rg_electron	64.34 Å
Forward intensity I(0) i0	9271690000.00
Molecular weight molecular_weight	802670.0 kDa
Excluded volume excluded_volume	997800 Å³
Envelope volume envelope_volume	1861600 Å³
Hydration-shell volume shell_volume	220310 Å³
Envelope diameter envelope_diameter	200.7 Å
Shell Rg shell_rg	78.69 Å
Envelope Rg envelope_rg	63.03 Å
Shape Rg shape_rg	64.39 Å
Total Rg total_rg	64.40 Å
Total atoms total_atoms	56559
Residues n_residues	7020
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	207.7 Å
Rg (real space) rg_real	64.52 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	9.2720e+09
I(0) uncertainty (real space) i0_real_error	1.5050e+08
Rg (reciprocal space) rg_reciprocal	65.67 Å
I(0) (reciprocal space) i0_reciprocal	9290000000.0000
Solution quality estimate total_estimate	0.8730
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	86.5 Å
Skewness Skewness skewness	0.005
Kurtosis Kurtosis kurtosis	-0.592
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0004
Highest regularization parameter α highest_alpha	7768000000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.874

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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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8. Citations (1)

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Unit-cell length a length_a	316.808 Å
Unit-cell length b length_b	316.808 Å
Unit-cell length c length_c	138.618 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	48

Space group space_group	P 42
Space-group number int_tables_number	77
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	14.998 Å
R factor r_factor	0.2952
R_work r_work	0.2950
R_free r_free	0.3147

Description description	Portal protein
Molecular weight formula_weight	70242.5 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	56559

Structure of the Immature Procapsid Conformation of P22 Portal Protein

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

Portal 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Enterobacteria phage P22
NCBI Class编号 ncbi_taxonomy_id	10754
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/jj/5jj1/5jj1.fit
pddf	/app/data/pr_computation/jj/5jj1/5jj1.pr.out
profile	/app/data/saxs_computation/jj/5jj1/5jj1.dat