SAXSdb — 2p7j

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

Putative sensory box/GGDEF family protein

Vibrio parahaemolyticus RIMD 2210633

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 SODIUM ION × 1 ACETIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q87SR8_VIBPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–287； UniProt 27–312 Author chain B； PDBConstruct 2–287； UniProt 27–312

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	2p7j
Deposition date deposition_date	2007-03-20
Structure title title	Crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus
Keywords keywords	;Sensory box/GGDEF family protein, Structural genomics, MCSG, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, TRANSCRIPTION ;; TRANSCRIPTION
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.

2p7j__assembly_1__model_1

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

Download this curve (.dat)

2p7j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p7j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.58 Å
Rg (electron density)	26.26 Å
Total Rg	27.04 Å
Atom count	4398
Residues	533
Excluded volume	78076 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p7j__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	Putative sensory box/GGDEF family protein
Molecular weight formula_weight	33306.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4836

NQKYQALLANNVENTAKEALHQLAYTGREYNNIQDQIETISDLLGHSQSLYDYLREPSKANLTILENMWSSVARNQKLYKQIRFLDTSGTEKVRIKYDFKTSIAGPSLILRDKSAREYFKYAQSLDNEQISAWGIELERDKGELVYPLSPSLRILMPISVNDVRQGYLVLNVDIEYLSSLLNYSPVRDFHIELVKHKGFYIASPDESRLYGDIIPERSQFNFSNMYPDIWPRVVSEQAGYSYSGEHLIAFSSIKFVSNEPLHLIIDLSNEQLSKRATRDINDLIQES

Source Source

Source organism organism	Vibrio parahaemolyticus RIMD 2210633
NCBI taxonomy ID ncbi_taxonomy_id	223926
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 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	321

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2p7ja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.2 — YkuI C-terminal domain-like

Domain ID domain_id	d2p7ja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.2 — YkuI C-terminal domain-like

Domain ID domain_id	d2p7jb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.2 — YkuI C-terminal domain-like

Domain ID domain_id	d2p7jb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.6 — Sensory domain-like
Family Family family	d.110.6.2 — YkuI C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	2p7jA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	2p7jA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	2p7jA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	2p7jB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	2p7jB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	2p7jB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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Unit-cell length a length_a	72.980 Å
Unit-cell length b length_b	81.596 Å
Unit-cell length c length_c	121.851 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	8

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	38.690 Å
R factor r_factor	0.1958
R_work r_work	0.1935
R_free r_free	0.2386

Crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus

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

Putative sensory box/GGDEF family protein

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

2p7j__assembly_1__model_1

2p7j__assembly_1__model_1 | I(q)

2p7j__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the domain of putative sensory box/GGDEF family protein from Vibrio parahaemolyticus

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

Putative sensory box/GGDEF family protein

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

2p7j__assembly_1__model_1

2p7j__assembly_1__model_1 | I(q)

2p7j__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)