SAXSdb — 6e8m

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

LeSH (Llo2327)

Legionella longbeachae serogroup 1 (strain NSW150)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–167	Not recorded	DnaJ-A1 pTyr381 peptide × 1 （P31689）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；296 K；PEG3000, malic acid, Tris-HCl	Resolution 1.61 Å R-free 0.212

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 6E8M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6E8H Legionella Longbeachae LeSH (Llo2327) Deposited 2018-07-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；278 K；Tris, PEG3000, sodium acetate	Resolution 1.68 Å R-free 0.247
6E8I Legionella Longbeachae LeSH (Llo2327) bound to phosphotyrosine Deposited 2018-07-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Not recorded	PTR O-PHOSPHOTYROSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；278 K；PEG3000, sodium acetate, Tris-HCl	Resolution 1.68 Å R-free 0.250
6E8K Legionella Longbeachae LeSH (Llo2327) bound to the human interleukin-2 receptor beta pTyr387 peptide Deposited 2018-07-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296 K；PEG3000, sodium malonate	Resolution 1.71 Å R-free 0.211

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

View Construct and Data Evidence

UniProt name	D3HJY4_LEGLN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–169； UniProt 1–167

DnaJ-A1 pTyr381 peptide

OrganismNot specified

UniProt P31689

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 375–387	Non-standard monomer：Yes (specific site not provided by mmCIF)	LeSH (Llo2327) × 1 （D3HJY4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；296 K；PEG3000, malic acid, Tris-HCl	Resolution 1.61 Å R-free 0.212

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 6E8M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LO1 NMR structure of the protein BC008182, a DNAJ-like domain from Homo sapiens Deposited 2012-01-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–70（70 aa） Fragment：J domain residues 1-70	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.080；Pressure ambient NMR sample composition 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 5 mM sodium azide, 50 mM sodium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2M6Y The solution structure of the J-domain of human DnaJA1 Deposited 2013-04-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–67（67 aa） Fragment：J-domain (UNP residues 1-67)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient NMR sample composition 1.03 mM [U-13C; U-15N] J-domain of DnaJA1, 20 mM MES, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 50 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	DNJA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 375–387

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	6e8m
Deposition date deposition_date	2018-07-30
Structure title title	Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 pTyr381 peptide
Keywords keywords	Src homology 2 domain, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING 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	17.99 Å
Radius of gyration Rg (electron density) rg_electron	16.83 Å
Forward intensity I(0) i0	6160370.00
Molecular weight molecular_weight	18744.0 kDa
Excluded volume excluded_volume	23844 Å³
Envelope volume envelope_volume	28314 Å³
Hydration-shell volume shell_volume	14590 Å³
Envelope diameter envelope_diameter	63.4 Å
Shell Rg shell_rg	22.36 Å
Envelope Rg envelope_rg	17.29 Å
Shape Rg shape_rg	16.79 Å
Total Rg total_rg	18.00 Å
Total atoms total_atoms	1323
Residues n_residues	158
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	17.95 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	6.1600e+06
I(0) uncertainty (real space) i0_real_error	9.1330e+04
Rg (reciprocal space) rg_reciprocal	17.95 Å
I(0) (reciprocal space) i0_reciprocal	6160000.0000
Solution quality estimate total_estimate	0.7962
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.245
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1036000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; 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	LeSH (Llo2327)
Molecular weight formula_weight	19771.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1469

GAMEAMQKNELNSKIPIIFGLINSYQIHNLLEQHNAKTKESKAVFLIRDSSTYPGLLTISYYCQEQDIVKHIRFGLTDKGWKTAPKPPHEPLKSDSPEIKEKYTLDKIKFERKMKQFINTAKKLFEQHIRAESFKTLIMELKIHEFNLEGLIKPTRSQASQEKHFTDYV

来源 Source

来源生物 organism	Legionella longbeachae serogroup 1 (strain NSW150)
NCBI Class编号 ncbi_taxonomy_id	661367
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DnaJ-A1 pTyr381 peptide
Molecular weight formula_weight	1698.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

HYNGEAYEDDEHH

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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8. Citations (1)

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Unit-cell length a length_a	40.900 Å
Unit-cell length b length_b	64.710 Å
Unit-cell length c length_c	67.850 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	24.210 Å
R factor r_factor	0.1992
R_work r_work	0.1986
R_free r_free	0.2123

fit	/app/data/saxs_computation/e8/6e8m/6e8m.fit
pddf	/app/data/pr_computation/e8/6e8m/6e8m.pr.out
profile	/app/data/saxs_computation/e8/6e8m/6e8m.dat

Legionella Longbeachae LeSH (Llo2327) bound to the human DnaJ-A1 pTyr381 peptide

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

LeSH (Llo2327)

State in the Current Structure

Other States of the Same Protein in the Database

DnaJ-A1 pTyr381 peptide

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)