SAXSdb — 5ms7

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

Legionella pneumophila effector protein RavZ

Legionella pneumophila subsp. pneumophila ATCC 33215

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 20–502	Not recorded	BA BARIUM ION × 4 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；16% PEG3350, 0.2 M BaCl2 and 0.1 M MES	Resolution 2.80 Å R-free 0.254

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 5MS7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CQC Crystal structure of the legionella pneumophila effector protein RavZ Deposited 2015-07-21	Different construct 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 10–458（449 aa）	Not recorded	BA BARIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277.15 K；12% PEG 3350, 0.2 M BaCl2, 0.1 M MES	Resolution 2.98 Å R-free 0.250
5HZY Crystal structure of the legionella pneumophila effector protein RavZ - P6322 Deposited 2016-02-03	Different construct Different mutation/modification 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 49–502（454 aa） Fragment：UNP residues 49-502	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.8M Sodium Acetate trihydrate, 200mM NaCl	Resolution 2.55 Å R-free 0.213
5HZY Crystal structure of the legionella pneumophila effector protein RavZ - P6322 Deposited 2016-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 49–502（454 aa） Fragment：UNP residues 49-502	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.8M Sodium Acetate trihydrate, 200mM NaCl	Resolution 2.55 Å R-free 0.213
5IO3 Crystal structure of the legionella pneumophila effector protein RavZ - I422 Deposited 2016-03-08	Different construct Different mutation/modification 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 1–502（502 aa）	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；2.2M NaCl, 28% PEG 3350, 0.1M Imidazole pH6.5	Resolution 2.74 Å R-free 0.287
5IZV Crystal structure of the legionella pneumophila effector protein RavZ - F222 Deposited 2016-03-26	Different construct Different mutation/modification 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 1–502（502 aa）	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2M NaCl, 20% PEG 3350, 0.1M MgCl2, 0.1M Imidazole pH 6.5	Resolution 2.81 Å R-free 0.227
5IZV Crystal structure of the legionella pneumophila effector protein RavZ - F222 Deposited 2016-03-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–502（502 aa）	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2M NaCl, 20% PEG 3350, 0.1M MgCl2, 0.1M Imidazole pH 6.5	Resolution 2.81 Å R-free 0.227
5IZV Crystal structure of the legionella pneumophila effector protein RavZ - F222 Deposited 2016-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–502（502 aa）	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2M NaCl, 20% PEG 3350, 0.1M MgCl2, 0.1M Imidazole pH 6.5	Resolution 2.81 Å R-free 0.227
5IZV Crystal structure of the legionella pneumophila effector protein RavZ - F222 Deposited 2016-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–502（502 aa）	Mutation：C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2M NaCl, 20% PEG 3350, 0.1M MgCl2, 0.1M Imidazole pH 6.5	Resolution 2.81 Å R-free 0.227
5MS2 Crystal structure of the Legionella pneumophila effector protein RavZ in complex with human LC3B Deposited 2016-12-30	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 A 1–431（431 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；0.17 M ammonium acetate, 0.085M tri sodium citrate, 25.5% PEG 4000 and 15% glycerol	Resolution 2.47 Å R-free 0.238
5MS5 Low-salt structure of RavZ LIR2-fused human LC3B Deposited 2016-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–36（13 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M citric acid anhydrous and 1.6 M ammonium sulfate	Resolution 1.53 Å R-free 0.242
5MS5 Low-salt structure of RavZ LIR2-fused human LC3B Deposited 2016-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–36（13 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M citric acid anhydrous and 1.6 M ammonium sulfate	Resolution 1.53 Å R-free 0.242
5MS8 Crystal structure of the legionella pneumophila effector protein RavZ_1-487 Deposited 2016-12-31	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–487（487 aa）	Not recorded	BA BARIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277.15 K；16% PEG3350, 0.2 M BaCl2 and 0.1 M MES	Resolution 2.85 Å R-free 0.249

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5ZUV9_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–485； UniProt 20–502

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	5ms7
Deposition date deposition_date	2016-12-31
Structure title title	Crystal structure of the legionella pneumophila effector protein RavZ_20-502
Keywords keywords	Hydrolase / Autophagy / Legionella pneumophila effector protein / ATG8 deconjugating enzyme, HYDROLASE; HYDROLASE
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	25.09 Å
Radius of gyration Rg (electron density) rg_electron	24.49 Å
Forward intensity I(0) i0	29249000.00
Molecular weight molecular_weight	41832.0 kDa
Excluded volume excluded_volume	52462 Å³
Envelope volume envelope_volume	64944 Å³
Hydration-shell volume shell_volume	23389 Å³
Envelope diameter envelope_diameter	95.8 Å
Shell Rg shell_rg	30.34 Å
Envelope Rg envelope_rg	25.13 Å
Shape Rg shape_rg	24.43 Å
Total Rg total_rg	25.40 Å
Total atoms total_atoms	2928
Residues n_residues	370
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	90.3 Å
Rg (real space) rg_real	25.24 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	2.9250e+07
I(0) uncertainty (real space) i0_real_error	4.5390e+05
Rg (reciprocal space) rg_reciprocal	25.19 Å
I(0) (reciprocal space) i0_reciprocal	29250000.0000
Solution quality estimate total_estimate	0.8174
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.558
Kurtosis Kurtosis kurtosis	-0.060
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5231000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.659; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.741; Smooth: 0.905

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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	Legionella pneumophila effector protein RavZ
Molecular weight formula_weight	54285.9 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	2942

GPGEQESDIDEFDLLEGDEKLPGDSELDKTTSIYPPETSWEVNKGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDSDYVAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQVLLTISYDPKSKQLTPTVYDSIGRDTYSESLSSYFKGKYRTTCDEILTQSIEKAIKSTDFTLGKFTRAAYNHQNRLTEGNCGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHVQDIESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEKSMLNFIGYSKTAKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESLQKLVLPCVKFDDTIDDFVTIEKDELFDVPDITGEELASKKGIEQGALDKEALLKQKQIKTDLLDLREEDKTGLKKPLHGGIKVK

来源 Source

来源生物 organism	Legionella pneumophila subsp. pneumophila ATCC 33215
NCBI Class编号 ncbi_taxonomy_id	933085
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	BARIUM ION
Molecular weight formula_weight	137.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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8. Citations (1)

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Unit-cell length a length_a	222.770 Å
Unit-cell length b length_b	222.770 Å
Unit-cell length c length_c	72.940 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 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.145 Å
R factor r_factor	0.2091
R_work r_work	0.2068
R_free r_free	0.2535

fit	/app/data/saxs_computation/ms/5ms7/5ms7.fit
pddf	/app/data/pr_computation/ms/5ms7/5ms7.pr.out
profile	/app/data/saxs_computation/ms/5ms7/5ms7.dat

Crystal structure of the legionella pneumophila effector protein RavZ_20-502

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

Legionella pneumophila effector protein RavZ

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