SAXSdb — 7xvk

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

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform

Arabidopsis thaliana

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–390	Not recorded	RxLR effector protein PSR2 × 1 （E0W4V5） 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

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 7XVK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 A 1–587（587 aa） Chain D 1–587（587 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 A 1–587（587 aa） Chain D 1–587（587 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 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 A 1–587（587 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 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 A 1–587（587 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

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	2AAB_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–390； UniProt 1–390

RxLR effector protein PSR2

Phytophthora sojae

UniProt E0W4V5

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 59–670	Not recorded	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform × 1 （Q38950） 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

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 7XVK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GNC Crystal structure of Phytophthora. sojae PSR2 Deposited 2016-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–670（612 aa） Fragment：UNP residues 59-670	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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
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 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 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	PSR2_PHYSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； 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	7xvk
Deposition date deposition_date	2022-05-24
Structure title title	Modularity of Phytophthora effectors enables host mimicry of a principal phosphatase
Keywords keywords	plant immunology, translocation, effector, phosphatase, IMMUNE SYSTEM; IMMUNE SYSTEM
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	48.50 Å
Radius of gyration Rg (electron density) rg_electron	50.89 Å
Forward intensity I(0) i0	171069000.00
Molecular weight molecular_weight	110070.0 kDa
Excluded volume excluded_volume	139210 Å³
Envelope volume envelope_volume	200630 Å³
Hydration-shell volume shell_volume	38489 Å³
Envelope diameter envelope_diameter	192.2 Å
Shell Rg shell_rg	44.64 Å
Envelope Rg envelope_rg	51.09 Å
Shape Rg shape_rg	50.89 Å
Total Rg total_rg	50.61 Å
Total atoms total_atoms	7754
Residues n_residues	990
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	180.7 Å
Rg (real space) rg_real	51.52 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	1.7230e+08
I(0) uncertainty (real space) i0_real_error	2.9530e+06
Rg (reciprocal space) rg_reciprocal	48.51 Å
I(0) (reciprocal space) i0_reciprocal	170800000.0000
Solution quality estimate total_estimate	0.5513
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.5 Å
Skewness Skewness skewness	0.679
Kurtosis Kurtosis kurtosis	-0.230
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	1.1760
Highest regularization parameter α highest_alpha	6473000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.586; Stabil: 0.900; Sysdev: 0.000; Positv: 1.000; Valcen: 0.407; Smooth: 0.317

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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	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform
Molecular weight formula_weight	43547.2 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	8729

MSMIDEPLYPIAVLIDELKNDDIQLRLNSIRRLSTIARALGEERTRKELIPFLSENNDDDDEVLLAMAEELGVFIPYVGGVEYAHVLLPPLETLSTVEETCVREKAVESLCRVGSQMRESDLVDHFISLVKRLAAGEWFTARVSACGVFHIAYPSAPDMLKTELRSLYTQLCQDDMPMVRRAAATNLGKFAATVESAHLKTDVMSMFEDLTQDDQDSVRLLAVEGCAALGKLLEPQDCVQHILPVIVNFSQDKSWRVRYMVANQLYELCEAVGPEPTRTELVPAYVRLLRDNEAEVRIAAAGKVTKFCRILNPEIAIQHILPCVKELSSDSSQHVRSALASVIMGMAPVLGKDATIEHLLPIFLSLLKDEFPDVRLNIISKLDQVNQVIG

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RxLR effector protein PSR2
Molecular weight formula_weight	68382.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SSVPGFEKLANLLKPKPGLKKLLKWADAKKPPETVFTRLRLDKTGTQLFDNTDFPVWAAYTRSVAQTDSEASAVMLKTLVSRYSDEVLSGMIAAAKKSSKTESIATKLETEQMRTWLAAKKTPDDMFLVFKLNKAGDDILSSPLLSAWTNYMKLSNKENPKAQTTLIATMTKHYGDSGVSQILAAARKSPATQSTAKRLEAEQVQLWLKKGRTPDDTFTLLSLDRAGDDLLASPQFNTWMKYINYYNKENPDEKTTVLAKLMTHFDDEELTPILVVARKVPSTESTAAKLQAEQFKNWLSADKSPEEAFTLLQLDKAGDDLLTNPQLTNWLKYTENFNLNKEINEQVTAIQVFRAQYVDDSRIANMVIAAEKVPNTQAIAKRVEDELFKGWTVVLNKPDDVFINLKLETVGENVFESPLWSFYTKFLEKYNTANPGKEQTMISGLARGYNDVTLTNMLLKAKEAPSTKTLATKLEDELVQYWLADKKLPDKLFGYLELKESVDGILTNPVFNVWLKYLNAFNDKAPVKKALMIDTLKSAFGDVAVSNMLFAAKKDPGTAKVAATLQTALLSKWVLEKKTPGQVSAILKEGAGADVSAKLLATYSAKFKVRWG

来源 Source

来源生物 organism	Phytophthora sojae
NCBI Class编号 ncbi_taxonomy_id	67593
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	831

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7xvkA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	76.211 Å
Unit-cell length b length_b	111.552 Å
Unit-cell length c length_c	161.756 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	38.770 Å
R factor r_factor	0.2093
R_work r_work	0.2088
R_free r_free	0.2267

fit	/app/data/saxs_computation/xv/7xvk/7xvk.fit
pddf	/app/data/pr_computation/xv/7xvk/7xvk.pr.out
profile	/app/data/saxs_computation/xv/7xvk/7xvk.dat

Modularity of Phytophthora effectors enables host mimicry of a principal phosphatase

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

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform

State in the Current Structure

Other States of the Same Protein in the Database

RxLR effector protein PSR2

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)