SAXSdb — 5io3

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

Uncharacterized protein RavZ

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

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 1–502	Mutation：C258S	No other associated polymer	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

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 5IO3	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 mutation/modification 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 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 oligomeric state 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
5IZV Crystal structure of the legionella pneumophila effector protein RavZ - F222 Deposited 2016-03-26	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 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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
5MS7 Crystal structure of the legionella pneumophila effector protein RavZ_20-502 Deposited 2016-12-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–502（483 aa）	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
5MS8 Crystal structure of the legionella pneumophila effector protein RavZ_1-487 Deposited 2016-12-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 1–502； UniProt 1–502

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	5io3
Deposition date deposition_date	2016-03-08
Structure title title	Crystal structure of the legionella pneumophila effector protein RavZ - I422
Keywords keywords	Autophagy, Atg8, deconjugating enzyme, protease, Atg4B, 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	25.13 Å
Radius of gyration Rg (electron density) rg_electron	24.48 Å
Forward intensity I(0) i0	30779000.00
Molecular weight molecular_weight	43120.0 kDa
Excluded volume excluded_volume	54207 Å³
Envelope volume envelope_volume	66459 Å³
Hydration-shell volume shell_volume	23766 Å³
Envelope diameter envelope_diameter	94.5 Å
Shell Rg shell_rg	30.42 Å
Envelope Rg envelope_rg	25.11 Å
Shape Rg shape_rg	24.46 Å
Total Rg total_rg	25.27 Å
Total atoms total_atoms	3038
Residues n_residues	385
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	87.7 Å
Rg (real space) rg_real	25.26 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	3.0780e+07
I(0) uncertainty (real space) i0_real_error	4.5410e+05
Rg (reciprocal space) rg_reciprocal	25.22 Å
I(0) (reciprocal space) i0_reciprocal	30780000.0000
Solution quality estimate total_estimate	0.5631
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.541
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	5205000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 0.120; Positv: 1.000; Valcen: 0.823; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein RavZ
Molecular weight formula_weight	56295.3 kDa
Mutation mutation	C258S
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	3071

MKGKLTGKDKLIVDEFEELGEQESDIDEFDLLEGDEKLPGDSELDKTTSIYPPETSWEVNKGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDSDYVAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQVLLTISYDPKSKQLTPTVYDSIGRDTYSESLSSYFKGKYRTTCDEILTQSIEKAIKSTDFTLGKFTRAAYNHQNRLTEGNSGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHVQDIESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEKSMLNFIGYSKTAKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESLQKLVLPCVKFDDTIDDFVTIEKDELFDVPDITGEELASKKGIEQGALDKEALLKQKQIKTDLLDLREEDKTGLKKPLHGGIKVK

来源 Source

来源生物 organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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8. Citations (1)

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Unit-cell length a length_a	222.041 Å
Unit-cell length b length_b	222.041 Å
Unit-cell length c length_c	71.298 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	2.740 Å
Low-resolution limit resolution_low	39.250 Å
R factor r_factor	0.2298
R_work r_work	0.2244
R_free r_free	0.2866

fit	/app/data/saxs_computation/io/5io3/5io3.fit
pddf	/app/data/pr_computation/io/5io3/5io3.pr.out
profile	/app/data/saxs_computation/io/5io3/5io3.dat

Crystal structure of the legionella pneumophila effector protein RavZ - I422

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

Uncharacterized 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)