SAXSdb — 4mxp

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

Defects in Rab1 recruitment protein A

Legionella pneumophila subsp. 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 330–647	Fragment：GEF and P4M domains, UNP residues 330-647	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

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 4MXP	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
3N6O Crystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila Deposited 2010-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 340–647（308 aa） Fragment：GEF and P4M domains (UNP residues 340-647)	Not recorded	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
3N6O Crystal structure of the GEF and P4M domain of DrrA/SidM from Legionella pneumophila Deposited 2010-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 340–647（308 aa） Fragment：GEF and P4M domains (UNP residues 340-647)	Not recorded	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

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

View Construct and Data Evidence

UniProt name	DRRA_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–328； UniProt 330–647

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4mxp
Deposition date deposition_date	2013-09-26
Structure title title	Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM
Keywords keywords	Protein-lipid complex, Guanine Nucleotide Exchange Factor, Rab1 binding, PI(4)P-BINDING PROTEIN; PI(4)P-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	24.58 Å
Radius of gyration Rg (electron density) rg_electron	24.12 Å
Forward intensity I(0) i0	22370400.00
Molecular weight molecular_weight	35564.0 kDa
Excluded volume excluded_volume	44437 Å³
Envelope volume envelope_volume	55177 Å³
Hydration-shell volume shell_volume	20695 Å³
Envelope diameter envelope_diameter	91.6 Å
Shell Rg shell_rg	29.38 Å
Envelope Rg envelope_rg	24.62 Å
Shape Rg shape_rg	24.11 Å
Total Rg total_rg	24.83 Å
Total atoms total_atoms	2491
Residues n_residues	310
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	87.3 Å
Rg (real space) rg_real	24.85 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	2.2370e+07
I(0) uncertainty (real space) i0_real_error	3.2810e+05
Rg (reciprocal space) rg_reciprocal	24.79 Å
I(0) (reciprocal space) i0_reciprocal	22370000.0000
Solution quality estimate total_estimate	0.8178
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.579
Kurtosis Kurtosis kurtosis	-0.172
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5049000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.686; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.615; Smooth: 0.957

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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	Defects in Rab1 recruitment protein A
Molecular weight formula_weight	37114.2 kDa
EC 编号 ec_number	2.7.7.-
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	2696

MGHHHHHHGSAKIRELGVQRVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILADFKDKLAEATDEQSLKQIVAELKSKDEYRILAKGQGLTTQLLGLKTSSVSSFEKMVEETRESIKSQERQTIKIK

来源 Source

来源生物 organism	Legionella pneumophila subsp. 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	;(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 ;
Molecular weight formula_weight	554.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	195

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4mxpA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	70 —

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8. Citations (1)

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Unit-cell length a length_a	128.552 Å
Unit-cell length b length_b	128.552 Å
Unit-cell length c length_c	53.222 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	26.900 Å
R factor r_factor	0.1896
R_work r_work	0.1886
R_free r_free	0.2079

fit	/app/data/saxs_computation/mx/4mxp/4mxp.fit
pddf	/app/data/pr_computation/mx/4mxp/4mxp.pr.out
profile	/app/data/saxs_computation/mx/4mxp/4mxp.dat

Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM

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

Defects in Rab1 recruitment protein A

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