SAXSdb — 6x6o

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

Protein spackle

Escherichia virus T4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–97	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；2.5 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.5, and 4 % (v/v) glycerol	Resolution 1.52 Å R-free 0.191
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–97	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；2.5 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.5, and 4 % (v/v) glycerol	Resolution 1.52 Å R-free 0.191

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 6X6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6XC0 Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–97（97 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SIN SUCCINIC ACID × 1 CL CHLORIDE ION × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5	Resolution 1.78 Å R-free 0.198
6XC0 Crystal structure of bacteriophage T4 spackle and lysozyme in monoclinic form Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–97（97 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5	Resolution 1.78 Å R-free 0.198
6XC1 Crystal structure of bacteriophage T4 spackle and lysozyme in orthorhombic form Deposited 2020-06-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–97（97 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 IPA ISOPROPYL ALCOHOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；35% (w/v) polyethylene glycol 3350, 20% 2-propanol, 0.1 M HEPES-NaOH pH 7.5	Resolution 1.92 Å R-free 0.215
7CN6 T4 phage spackle protein gp61.3 Deposited 2020-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–97（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.4；293.15 K；PEG4000, glycine, calcium chloride	Resolution 1.60 Å R-free 0.228
7CN6 T4 phage spackle protein gp61.3 Deposited 2020-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–97（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.4；293.15 K；PEG4000, glycine, calcium chloride	Resolution 1.60 Å R-free 0.228
7CN6 T4 phage spackle protein gp61.3 Deposited 2020-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–97（75 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.4；293.15 K；PEG4000, glycine, calcium chloride	Resolution 1.60 Å R-free 0.228
7CN7 T4 phage spackle protein gp61.3 complex with lysozyme domain of gp5 tail lysozyme Deposited 2020-07-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–97（75 aa）	Not recorded	1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 1 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；PEG550MME, MES, KSCN	Resolution 1.15 Å R-free 0.121

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

View Construct and Data Evidence

UniProt name	SPAC_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 1–97 Author chain B； PDBConstruct 1–97； UniProt 1–97

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	6x6o
Deposition date deposition_date	2020-05-28
Structure title title	Crystal structure of T4 protein Spackle as determined by native SAD phasing
Keywords keywords	APOBEC, deaminase, HYDROLASE, 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	18.26 Å
Radius of gyration Rg (electron density) rg_electron	17.30 Å
Forward intensity I(0) i0	6228900.00
Molecular weight molecular_weight	17385.0 kDa
Excluded volume excluded_volume	21435 Å³
Envelope volume envelope_volume	25651 Å³
Hydration-shell volume shell_volume	13154 Å³
Envelope diameter envelope_diameter	63.4 Å
Shell Rg shell_rg	22.28 Å
Envelope Rg envelope_rg	17.59 Å
Shape Rg shape_rg	17.25 Å
Total Rg total_rg	18.31 Å
Total atoms total_atoms	2377
Residues n_residues	149
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	61.6 Å
Rg (real space) rg_real	18.27 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	6.2290e+06
I(0) uncertainty (real space) i0_real_error	8.2360e+04
Rg (reciprocal space) rg_reciprocal	18.27 Å
I(0) (reciprocal space) i0_reciprocal	6229000.0000
Solution quality estimate total_estimate	0.8029
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.326
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1176000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein spackle
Molecular weight formula_weight	12075.8 kDa
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	2530

MKKFIFATIFALASCAAQPAMAGYDKDLCEWSMTADQTEVETQIEADIMNIVKRDRPEMKAEVQKQLKSGGVMQYNYVLYCDKNFNNKNIIAEVVGELEHHHHHH

来源 Source

来源生物 organism	Escherichia virus T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

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8. Citations (1)

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Unit-cell length a length_a	44.424 Å
Unit-cell length b length_b	79.822 Å
Unit-cell length c length_c	93.227 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.520 Å
Low-resolution limit resolution_low	40.104 Å
R factor r_factor	0.1742
R_work r_work	0.1733
R_free r_free	0.1907

fit	/app/data/saxs_computation/x6/6x6o/6x6o.fit
pddf	/app/data/pr_computation/x6/6x6o/6x6o.pr.out
profile	/app/data/saxs_computation/x6/6x6o/6x6o.dat

Crystal structure of T4 protein Spackle as determined by native SAD phasing

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

Protein spackle

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