SAXSdb — 8bvp

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

Restriction endonuclease

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 37–573	Not recorded	EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；100 mM Tris-HCl ph 8.5, 14 % ethanol	Resolution 2.10 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 8BVP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8JHU Legionella effector protein SidI Deposited 2023-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–942（942 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5ZSL3_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–542； UniProt 37–573

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	8bvp
Deposition date deposition_date	2022-12-05
Structure title title	Crystal structure of an N-terminal fragment of the effector protein Lpg2504 (SidI) from Legionella pneumophila
Keywords keywords	bacterial effector, glycosyl transferase, Legionella pneumophila, translation inhibition, 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	27.64 Å
Radius of gyration Rg (electron density) rg_electron	26.79 Å
Forward intensity I(0) i0	60638700.00
Molecular weight molecular_weight	61200.0 kDa
Excluded volume excluded_volume	76967 Å³
Envelope volume envelope_volume	97119 Å³
Hydration-shell volume shell_volume	30440 Å³
Envelope diameter envelope_diameter	97.5 Å
Shell Rg shell_rg	33.78 Å
Envelope Rg envelope_rg	26.64 Å
Shape Rg shape_rg	26.77 Å
Total Rg total_rg	27.63 Å
Total atoms total_atoms	4320
Residues n_residues	532
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	93.7 Å
Rg (real space) rg_real	27.54 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	6.0640e+07
I(0) uncertainty (real space) i0_real_error	9.5700e+05
Rg (reciprocal space) rg_reciprocal	27.58 Å
I(0) (reciprocal space) i0_reciprocal	60640000.0000
Solution quality estimate total_estimate	0.8807
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.8 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.317
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	12160000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.981

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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	Restriction endonuclease
Molecular weight formula_weight	62175.1 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	4654

GGAMSIPCKWLKKDKGDYSIPFPTGTTSIPEETIPSAIVLQPVANENTVISGYKLKDTVSSPEKAQEVNNKTVSPRTPKIIVKHDNSLQSLTIMDIYSQKPIQFDESKVDEIIHSLETKKVNLEKAIEDNNAELSKIKKQKSKLAYLTRLYKENKENIQDYCTLNEYIEAHLFNPKFLSRHEKALNNFKALKSQFTGPVNLKELEKLTDKLTGIKEYSYDFHSNSLPYDLEHDKSFRNFYDFDGLKESIESIIKELEVLNSIRQAVSDKYPNSFKALNETEEHDDKLKFINIIFNDGFSTTYDQQTFIKALSALDIEKAIDAYTNVKNKLENTQDIIANKEGCRNKLISELQTLIANKQEPYLSANEKLGGFYSKRKLSASEGFHLAYQANRRDPIKPEVIENIITKMKPIDEDTHLDIHIRPPDCGVFITPEDIKKFQEAGIKVNITIHEYKQNYTRRYLQQYTHDLMRQANSVQFFNAEDRENAIIAATYGDCDKRNTTEPTGVAKKIREVGEDFDLDKYPVQKYDLKGKSGLTVASQKL

来源 Source

来源生物 organism	Legionella pneumophila
NCBI Class编号 ncbi_taxonomy_id	446
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	331

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8. Citations (1)

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Unit-cell length a length_a	108.700 Å
Unit-cell length b length_b	61.030 Å
Unit-cell length c length_c	113.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	36.120 Å
R factor r_factor	0.2091
R_work r_work	0.2067
R_free r_free	0.2541

fit	/app/data/saxs_computation/bv/8bvp/8bvp.fit
pddf	/app/data/pr_computation/bv/8bvp/8bvp.pr.out
profile	/app/data/saxs_computation/bv/8bvp/8bvp.dat

Crystal structure of an N-terminal fragment of the effector protein Lpg2504 (SidI) from Legionella pneumophila

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

Restriction endonuclease

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