SAXSdb — 6p5h

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

MavC

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 126–225	Fragment：middle insertion domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.5；294 K；2 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M CAPS: NaOH	Resolution 1.53 Å R-free 0.224
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 126–225	Fragment：middle insertion domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 10.5；294 K；2 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M CAPS: NaOH	Resolution 1.53 Å R-free 0.224

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 6P5H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6K3B Crystal structure of Lpg2147-Lpg2149 complex Deposited 2019-05-17	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 7–384（378 aa）	Mutation：C74A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG3350, ammonium nitrate	Resolution 1.97 Å R-free 0.205
6KFP Crystal structure of MavC ternary complex Deposited 2019-07-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–384（378 aa）	Mutation：C74A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350, lithium chloride	Resolution 2.92 Å R-free 0.250
6KG6 Crystal structure of MavC/UBE2N-Ub complex Deposited 2019-07-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 7–384（378 aa）	Mutation：C74A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 4000, Tris	Resolution 2.39 Å R-free 0.245
6KL4 Crystal structure of MavC-UBE2N-Ub Deposited 2019-07-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–384（378 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；289.15 K；0.2M Sodium malonate pH 6.0, 20%w/v PEG 3,350	Resolution 2.85 Å R-free 0.262
6P5B Crystal Structure of MavC in Complex with Ub-UbE2N Deposited 2019-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–384（384 aa）	Mutation：C74A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；0.2 M Na Malonate, 25% PEG 3350, 10 mM NiCl2	Resolution 2.10 Å R-free 0.232
6UMP Crystal structure of MavC in complex with substrate mimic in P65 space group Deposited 2019-10-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–384（384 aa）	Mutation：C74A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium formate, 20% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.304
6UMS Crystal structure of MavC in complex with its substrate mimic in C222(1) space group Deposited 2019-10-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–384（384 aa）	Mutation：C74A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.15 M Potassium bromide, 30% (w/v) PEG 2000 MME	Resolution 2.34 Å R-free 0.250

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

View Construct and Data Evidence

UniProt name	A0A2S6F4I5_LEGPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–105； UniProt 126–225 Author chain B； PDBConstruct 6–105； UniProt 126–225

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	6p5h
Deposition date deposition_date	2019-05-30
Structure title title	Structure of MavC middle insertion domain
Keywords keywords	UbE2N, Effector, MavC, PROTEIN BINDING; PROTEIN BINDING
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	19.60 Å
Radius of gyration Rg (electron density) rg_electron	18.58 Å
Forward intensity I(0) i0	9294680.00
Molecular weight molecular_weight	22992.0 kDa
Excluded volume excluded_volume	28916 Å³
Envelope volume envelope_volume	34616 Å³
Hydration-shell volume shell_volume	16082 Å³
Envelope diameter envelope_diameter	63.1 Å
Shell Rg shell_rg	23.97 Å
Envelope Rg envelope_rg	18.71 Å
Shape Rg shape_rg	18.60 Å
Total Rg total_rg	19.41 Å
Total atoms total_atoms	1620
Residues n_residues	196
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	62.5 Å
Rg (real space) rg_real	19.57 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	9.2950e+06
I(0) uncertainty (real space) i0_real_error	1.1730e+05
Rg (reciprocal space) rg_reciprocal	19.58 Å
I(0) (reciprocal space) i0_reciprocal	9295000.0000
Solution quality estimate total_estimate	0.8209
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.269
Kurtosis Kurtosis kurtosis	-0.492
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2123000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; 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)

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8. Citations (1)

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Unit-cell length a length_a	52.027 Å
Unit-cell length b length_b	52.027 Å
Unit-cell length c length_c	79.753 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	39.229 Å
R factor r_factor	0.2000
R_work r_work	0.1986
R_free r_free	0.2240

Description description	MavC
Molecular weight formula_weight	12248.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1981

Structure of MavC middle insertion domain

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

MavC

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)

来源生物 organism	Legionella pneumophila
NCBI Class编号 ncbi_taxonomy_id	446
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	361

fit	/app/data/saxs_computation/p5/6p5h/6p5h.fit
pddf	/app/data/pr_computation/p5/6p5h/6p5h.pr.out
profile	/app/data/saxs_computation/p5/6p5h/6p5h.dat