SAXSdb — 5jp1

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

Xanthomonas outer protein D

Xanthomonas campestris pv. vesicatoria (strain 85-10)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Small ubiquitin-related modifier × 1 （Q9SMD1） MALONATE ION × 2 (4S,5S)-1,2-DITHIANE-4,5-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3BYJ5_XANC5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–220； UniProt 298–515

Small ubiquitin-related modifier

Solanum lycopersicum

UniProt Q9SMD1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Xanthomonas outer protein D × 1 （Q3BYJ5） MALONATE ION × 2 (4S,5S)-1,2-DITHIANE-4,5-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9SMD1_SOLLC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–95； UniProt 1–95

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	5jp1
Deposition date deposition_date	2016-05-03
Structure title title	Structure of Xanthomonas campestris effector protein XopD bound to tomato SUMO
Keywords keywords	Enzyme, CE clan, Deubiquitinase, DeSUMOylase, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5jp1__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5jp1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jp1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.43 Å
Rg (electron density)	19.36 Å
Total Rg	20.23 Å
Atom count	2184
Residues	276
Excluded volume	38198 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jp1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Xanthomonas outer protein D
Molecular weight formula_weight	24438.2 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	2398

GPHGTQTPMGYSAMTPERIDVDNLPSPQDVADPELPPVRATSWLLDGHLRAYTDDLARRLRGEPNAHLLHFADSQVVTMLSSADPDQQARAQRLLAGDDIPPIVFLPINQPNAHWSLLVVDRRNKDAVAAYHYDSMAQKDPQQRYLADMAAYHLGLDYQQTHEMPIAIQSDGYSCGDHVLTGIEVLAHRVLDGTFDYAGGRDLTDIEPDRGLIRDRLAQA

Source Source

Source organism organism	Xanthomonas campestris pv. vesicatoria (strain 85-10)
NCBI taxonomy ID ncbi_taxonomy_id	316273
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Small ubiquitin-related modifier
Molecular weight formula_weight	10879.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSASGGTGDEDKKPNDQMVHINLKVKGQDGNEVFFRIKRSTQMRKLMNAYCDRQSVDMNSIAFLFDGRRLRAEQTPDELEMEEGDEIDAMLHQTGX

Source Source

Source organism organism	Solanum lycopersicum
Common name common_name	Tomato
NCBI taxonomy ID ncbi_taxonomy_id	4081
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(4S,5S)-1,2-DITHIANE-4,5-DIOL
Molecular weight formula_weight	152.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5jp1b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d5jp1b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	5jp1A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

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Unit-cell length a length_a	119.103 Å
Unit-cell length b length_b	119.103 Å
Unit-cell length c length_c	50.463 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 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	59.551 Å
R factor r_factor	0.1832
R_work r_work	0.1813
R_free r_free	0.2168

Structure of Xanthomonas campestris effector protein XopD bound to tomato SUMO

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

Xanthomonas outer protein D

State in the Current Structure

Other States of the Same Protein in the Database

Small ubiquitin-related modifier

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5jp1__assembly_1__model_1

5jp1__assembly_1__model_1 | I(q)

5jp1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of Xanthomonas campestris effector protein XopD bound to tomato SUMO

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

Xanthomonas outer protein D

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ubiquitin-related modifier

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5jp1__assembly_1__model_1

5jp1__assembly_1__model_1 | I(q)

5jp1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)