SAXSdb — 5gnc

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

Avh146

Phytophthora sojae

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 59–670	Fragment：UNP residues 59-670 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2M NH4COOH	Resolution 2.80 Å R-free 0.266

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 5GNC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7XVK Modularity of Phytophthora effectors enables host mimicry of a principal phosphatase Deposited 2022-05-24	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 59–670（612 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；5% PEG 20000 0.1 M Bis tris pH 5.8 5 mM MgSO4	Resolution 2.29 Å R-free 0.227
9J5I Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease Deposited 2024-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–670（670 aa） Chain E 1–670（670 aa）	Not recorded	MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å
9J5K Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease Deposited 2024-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–670（670 aa） Chain E 1–670（670 aa）	Not recorded	MN MANGANESE (II) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9J5N Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease Deposited 2024-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–670（670 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9J5R Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease Deposited 2024-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–670（670 aa）	Not recorded	MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	E0W4V5_PHYSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–612； UniProt 59–670

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	5gnc
Deposition date deposition_date	2016-07-20
Structure title title	Crystal structure of Phytophthora. sojae PSR2
Keywords keywords	PSR2, RNAi, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	48.85 Å
Radius of gyration Rg (electron density) rg_electron	51.73 Å
Forward intensity I(0) i0	65224000.00
Molecular weight molecular_weight	67330.0 kDa
Excluded volume excluded_volume	84903 Å³
Envelope volume envelope_volume	124220 Å³
Hydration-shell volume shell_volume	25148 Å³
Envelope diameter envelope_diameter	188.9 Å
Shell Rg shell_rg	40.03 Å
Envelope Rg envelope_rg	52.61 Å
Shape Rg shape_rg	51.67 Å
Total Rg total_rg	51.30 Å
Total atoms total_atoms	4702
Residues n_residues	584
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	180.6 Å
Rg (real space) rg_real	50.55 Å
Rg uncertainty (real space) rg_real_error	4.12 Å
I(0) (real space) i0_real	6.5220e+07
I(0) uncertainty (real space) i0_real_error	1.5760e+06
Rg (reciprocal space) rg_reciprocal	48.86 Å
I(0) (reciprocal space) i0_reciprocal	65080000.0000
Solution quality estimate total_estimate	0.5846
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	22.6 Å
Skewness Skewness skewness	0.661
Kurtosis Kurtosis kurtosis	-0.394
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1996000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.086; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.027; Smooth: 0.316

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	86.320 Å
Unit-cell length b length_b	49.720 Å
Unit-cell length c length_c	94.450 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2117
R_work r_work	0.2085
R_free r_free	0.2664

Description description	Avh146
Molecular weight formula_weight	68991.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4702

Crystal structure of Phytophthora. sojae PSR2

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

Avh146

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Phytophthora sojae
通用名 common_name	Soybean stem and root rot agent
NCBI Class编号 ncbi_taxonomy_id	67593
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/gn/5gnc/5gnc.fit
pddf	/app/data/pr_computation/gn/5gnc/5gnc.pr.out
profile	/app/data/saxs_computation/gn/5gnc/5gnc.dat