SAXSdb — 6ggo

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

Bacteriophage virulence determinant

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

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 20–228 Chain B； UniProt 20–228	Not recorded	ZN ZINC ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；GtgA, at a concentration of 24 mg/ml, was crystallyzed in 0.1 M Tris pH 8.5, 25% (v/v) isopropanol and 20% (w/v) PEG 3350	Resolution 2.60 Å R-free 0.255

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 6GGO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GGR Crystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65 Deposited 2018-05-03	Different construct Different mutation/modification 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 20–228（209 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallyzation conditions: 0.1 M Tris pH 8.3, 0.5 M LiCl and 32.5% (w/v) PEG 6000	Resolution 2.10 Å R-free 0.252

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

View Construct and Data Evidence

UniProt name	A0A0F6AZI6_SALT1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–212； UniProt 20–228 Author chain B； PDBConstruct 4–212； UniProt 20–228

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	6ggo
Deposition date deposition_date	2018-05-03
Structure title title	Crystal structure of Salmonella zinc metalloprotease effector GtgA
Keywords keywords	Protease, Metalloprotease, zinc, METAL BINDING PROTEIN; METAL 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	25.74 Å
Radius of gyration Rg (electron density) rg_electron	24.98 Å
Forward intensity I(0) i0	38984400.00
Molecular weight molecular_weight	45362.0 kDa
Excluded volume excluded_volume	55444 Å³
Envelope volume envelope_volume	69607 Å³
Hydration-shell volume shell_volume	24281 Å³
Envelope diameter envelope_diameter	87.4 Å
Shell Rg shell_rg	31.19 Å
Envelope Rg envelope_rg	25.20 Å
Shape Rg shape_rg	25.02 Å
Total Rg total_rg	25.58 Å
Total atoms total_atoms	6142
Residues n_residues	397
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	86.3 Å
Rg (real space) rg_real	25.87 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	3.8980e+07
I(0) uncertainty (real space) i0_real_error	5.3320e+05
Rg (reciprocal space) rg_reciprocal	25.83 Å
I(0) (reciprocal space) i0_reciprocal	38980000.0000
Solution quality estimate total_estimate	0.8645
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.489
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7640000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.969

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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	Bacteriophage virulence determinant
Molecular weight formula_weight	24098.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	6199

GAMSHPHDSKVFPDLPEHQDNPSQLRLQHDGLATDDKARLEPMCLAEYLISGPGGMDPDIEIDDDTYDECREVLSRILEDAYTQSGTFRRLMNYAYDQELHDVEQRWLLGAGENFGTTVTDEDLESSEGRKVIALNLDDTDDDSIPEYYESNDGPQQFDTTRSFIHQVVHALTHLQDKEDSNPRGPVVEYTNIILKEMGHTSPPRIAYEFSN

来源 Source

来源生物 organism	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NCBI Class编号 ncbi_taxonomy_id	588858
宿主生物 host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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8. Citations (1)

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Unit-cell length a length_a	95.783 Å
Unit-cell length b length_b	40.678 Å
Unit-cell length c length_c	112.161 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	75.300 Å
R factor r_factor	0.2192
R_work r_work	0.2175
R_free r_free	0.2553

fit	/app/data/saxs_computation/gg/6ggo/6ggo.fit
pddf	/app/data/pr_computation/gg/6ggo/6ggo.pr.out
profile	/app/data/saxs_computation/gg/6ggo/6ggo.dat

Crystal structure of Salmonella zinc metalloprotease effector GtgA

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

Bacteriophage virulence determinant

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