SAXSdb — 3n6o

▼

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

guanine nucleotide exchange factor

Legionella pneumophila

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 340–647	Fragment：GEF and P4M domains (UNP residues 340-647)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；298 K；20% (w/v) PEG4000, 0.16 M ammonium sulfate, 0.1 M sodium acetate, 20% glycerol, pH 4.8, vapor diffusion, hanging drop, temperature 298K	Resolution 2.50 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 340–647	Fragment：GEF and P4M domains (UNP residues 340-647)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；298 K；20% (w/v) PEG4000, 0.16 M ammonium sulfate, 0.1 M sodium acetate, 20% glycerol, pH 4.8, vapor diffusion, hanging drop, temperature 298K	Resolution 2.50 Å R-free 0.236

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 3N6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JZ9 Crystal structure of the GEF domain of DrrA/SidM from Legionella pneumophila Deposited 2009-09-23	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 340–533（194 aa） Fragment：GEF domain: UNP residues 340-533	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.25 M Sodium sulfate, 21% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.80 Å R-free 0.198
3JZA Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila Deposited 2009-09-23	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 B 340–533（194 aa） Fragment：GEF domain: UNP residues 340-533	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；292 K；0.1 M Sodium citrate, 35% v/v PEG 600, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.80 Å R-free 0.234
4MXP Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM Deposited 2013-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–647（318 aa） Fragment：GEF and P4M domains, UNP residues 330-647	Not recorded	DB4 (2R)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；4-6% PEG 3350, 100 mM Tris, 0.5 M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.83 Å R-free 0.208

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

View Construct and Data Evidence

UniProt name	Q5ZSQ3_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–311； UniProt 340–647 Author chain B； PDBConstruct 4–311； UniProt 340–647

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3n6o
Deposition date deposition_date	2010-05-26
Structure title title	Crystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila
Keywords keywords	phosphatidylinositol-4-phosphate, membrane, GEF, Rab, LCV, P4M, RabGEF, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	31.94 Å
Radius of gyration Rg (electron density) rg_electron	31.37 Å
Forward intensity I(0) i0	79844300.00
Molecular weight molecular_weight	68432.0 kDa
Excluded volume excluded_volume	84973 Å³
Envelope volume envelope_volume	116100 Å³
Hydration-shell volume shell_volume	32069 Å³
Envelope diameter envelope_diameter	116.7 Å
Shell Rg shell_rg	36.67 Å
Envelope Rg envelope_rg	31.34 Å
Shape Rg shape_rg	31.34 Å
Total Rg total_rg	31.93 Å
Total atoms total_atoms	4787
Residues n_residues	604
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	114.9 Å
Rg (real space) rg_real	31.99 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	7.9840e+07
I(0) uncertainty (real space) i0_real_error	1.2510e+06
Rg (reciprocal space) rg_reciprocal	31.97 Å
I(0) (reciprocal space) i0_reciprocal	79840000.0000
Solution quality estimate total_estimate	0.8650
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.4 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.394
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11990000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.989

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	guanine nucleotide exchange factor
Molecular weight formula_weight	35125.0 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	4966

GHMVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILADFKDKLAEATDEQSLKQIVAELKSKDEYRILAKGQGLTTQLLGLKTSSVSSFEKMVEETRESIKSQERQTIKIK

来源 Source

来源生物 organism	Legionella pneumophila
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3n6oA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	3n6oB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	74.962 Å
Unit-cell length b length_b	75.375 Å
Unit-cell length c length_c	130.965 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	8

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.1730
R_work r_work	0.1700
R_free r_free	0.2360

fit	/app/data/saxs_computation/n6/3n6o/3n6o.fit
pddf	/app/data/pr_computation/n6/3n6o/3n6o.pr.out
profile	/app/data/saxs_computation/n6/3n6o/3n6o.dat

Crystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila

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

guanine nucleotide exchange factor

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