SAXSdb — 4zkp

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

Tail needle protein gp26

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–233	Mutation：L222M	CA CALCIUM ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；40% PEG 1000, 0.1M MOPS pH7.0	Resolution 2.10 Å R-free 0.189
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–233	Mutation：L222M	CA CALCIUM ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；40% PEG 1000, 0.1M MOPS pH7.0	Resolution 2.10 Å R-free 0.189

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 4ZKP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C9I Structure of P22 Tail-Needle GP26 Bound to Xenon Gas Deposited 2008-02-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–233（233 aa） Chain B 1–233（233 aa） Chain C 1–233（233 aa）	Mutation：L222M Mutation：L222M Mutation：L222M	XE XENON × 7 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；298 K；18% PEG 4000, 0.1M Ammonium Sulfate, 0.1M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 4.60	Resolution 1.95 Å R-free 0.269
3C9I Structure of P22 Tail-Needle GP26 Bound to Xenon Gas Deposited 2008-02-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1–233（233 aa） Chain E 1–233（233 aa） Chain F 1–233（233 aa）	Mutation：L222M Mutation：L222M Mutation：L222M	XE XENON × 7 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；298 K；18% PEG 4000, 0.1M Ammonium Sulfate, 0.1M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 4.60	Resolution 1.95 Å R-free 0.269
4ZKU P22 Tail Needle Gp26 crystallized at pH 10.0 Deposited 2015-04-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–233（233 aa）	Mutation：L222M	CL CHLORIDE ION × 3 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；40% PEG 4000, 0.1M CAPS pH 10.0	Resolution 2.50 Å R-free 0.225
4ZKU P22 Tail Needle Gp26 crystallized at pH 10.0 Deposited 2015-04-30	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 1–233（233 aa）	Mutation：L222M	CL CHLORIDE ION × 3 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；40% PEG 4000, 0.1M CAPS pH 10.0	Resolution 2.50 Å R-free 0.225
4ZXQ P22 Tail Needle Gp26 1-140 crystallized at pH 3.9 Deposited 2015-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–140（140 aa） Chain B 1–140（140 aa） Chain C 1–140（140 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293 K；20% PEG 8000, 0.05 M Potassium phosphate monobasic pH 3.9	Resolution 2.75 Å R-free 0.252
4ZXQ P22 Tail Needle Gp26 1-140 crystallized at pH 3.9 Deposited 2015-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1–140（140 aa） Chain E 1–140（140 aa） Chain F 1–140（140 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.9；293 K；20% PEG 8000, 0.05 M Potassium phosphate monobasic pH 3.9	Resolution 2.75 Å R-free 0.252
8EAP Cryo-EM structure of the in-situ gp10-gp26 from bacteriophage P22 Deposited 2022-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 3–64（62 aa） Chain B 3–64（62 aa） Chain C 3–64（62 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

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

View Construct and Data Evidence

UniProt name	NEEDL_BPP22
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–237； UniProt 1–233 Author chain B； PDBConstruct 5–237； UniProt 1–233

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	4zkp
Deposition date deposition_date	2015-04-30
Structure title title	P22 Tail Needle Gp26 crystallized at pH 7.0
Keywords keywords	Viral protein, P22, Tail Needle, Membrane penetration; 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	84.84 Å
Radius of gyration Rg (electron density) rg_electron	90.01 Å
Forward intensity I(0) i0	25371100.00
Molecular weight molecular_weight	38327.0 kDa
Excluded volume excluded_volume	47112 Å³
Envelope volume envelope_volume	121940 Å³
Hydration-shell volume shell_volume	17831 Å³
Envelope diameter envelope_diameter	329.6 Å
Shell Rg shell_rg	41.05 Å
Envelope Rg envelope_rg	90.55 Å
Shape Rg shape_rg	90.03 Å
Total Rg total_rg	87.75 Å
Total atoms total_atoms	2688
Residues n_residues	358
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	256.6 Å
Rg (real space) rg_real	81.26 Å
Rg uncertainty (real space) rg_real_error	2.59 Å
I(0) (real space) i0_real	2.4860e+07
I(0) uncertainty (real space) i0_real_error	5.5660e+05
Rg (reciprocal space) rg_reciprocal	75.29 Å
I(0) (reciprocal space) i0_reciprocal	24720000.0000
Solution quality estimate total_estimate	0.6279
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.489
Kurtosis Kurtosis kurtosis	-0.715
Angular range angular_range	— – 0.0900 Å⁻¹
Current regularization parameter α current_alpha	0.0330
Highest regularization parameter α highest_alpha	5780000.0000
Real-space data points n_real_points	19
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.013; Stabil: 0.969; Sysdev: 1.000; Positv: 1.000; Valcen: 0.139; Smooth: 0.804

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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	Tail needle protein gp26
Molecular weight formula_weight	25075.7 kDa
Mutation mutation	L222M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3452

GPGSMADPSLNNPVVIQATRLDASILPRNVFSKSYLLYVIAQGTDVGAIAGKANEAGQGAYDAQVKNDEQDVELADHEARIKQLRIDVDDHESRITANTKAITALNVRVTTAEGEIASLQTNVSALDGRVTTAENNISALQADYVSKTATTSQSLASPLNVTTSYSVGGKKVLGARQTGWTAATGTANKGVFDADLTFAVSDTYTQSEIQAIANALITERRRTKAMEDALRAHGLID

来源 Source

来源生物 organism	Enterobacteria phage P22
NCBI Class编号 ncbi_taxonomy_id	10754
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	764

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4zkpA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	4zkpA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	940 —

Domain ID domain_id	4zkpB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	340 —

Domain ID domain_id	4zkpB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	940 —

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8. Citations (1)

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Unit-cell length a length_a	43.846 Å
Unit-cell length b length_b	43.846 Å
Unit-cell length c length_c	272.319 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.120 Å
R factor r_factor	0.1580
R_work r_work	0.1540
R_free r_free	0.1890

fit	/app/data/saxs_computation/zk/4zkp/4zkp.fit
pddf	/app/data/pr_computation/zk/4zkp/4zkp.pr.out
profile	/app/data/saxs_computation/zk/4zkp/4zkp.dat

P22 Tail Needle Gp26 crystallized at pH 7.0

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

Tail needle protein gp26

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