SAXSdb — 2pig

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

Putative transferase

Salmonella paratyphi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5PHU6_SALPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 1–326 Author chain B； PDBConstruct 1–326； UniProt 1–326

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	2pig
Deposition date deposition_date	2007-04-13
Structure title title	Crystal structure of ydcK from Salmonella cholerae at 2.38 A resolution. Northeast Structural Genomics target SCR6
Keywords keywords	scr6, nesg, ydcK, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, TRANSFERASE; TRANSFERASE
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.

2pig__assembly_1__model_1

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

Download this curve (.dat)

2pig__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pig__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.45 Å
Rg (electron density)	29.20 Å
Total Rg	29.61 Å
Atom count	4889
Residues	627
Excluded volume	85955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pig__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 (3)

Entity 1 Entity 1 polymer

Description description	Putative transferase
Molecular weight formula_weight	37129.2 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	5024

MTKYRLSEGPRAFTYQVDGEKKSVLLRQVIAVTDFNDVKAGTSGGWVDADNVLSQQGDCWIYDENAMAFAGTEITGNARITQPCTLYNNVRIGDNVWIDRADISDGARISDNVTIQSSSVREECAIYGDARVLNQSEILAIQGLTHEHAQILQIYDRATVNHSRIVHQVQLYGNATITHAFIEHRAEVFDFALIEGDKDNNVWICDCAKVYGHARVIAGTEEDAIPTLRYSSQVAEHALIEGNCVLKHHVLVGGHAEVRGGPILLDDRVLIEGHACIQGEILIERQVEISGRAAVIAFDDNTIHLRGPKVINGEDRITRTPLVGSLLEHHHHHH

Source Source

Source organism organism	Salmonella paratyphi
NCBI taxonomy ID ncbi_taxonomy_id	54388
Host organism host_organism	Escherichia coli

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	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2piga_
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.7 — YdcK-like

Domain ID domain_id	d2pigb1
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.7 — YdcK-like

Domain ID domain_id	d2pigb2
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

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Unit-cell length a length_a	103.603 Å
Unit-cell length b length_b	103.603 Å
Unit-cell length c length_c	160.577 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2195
R_work r_work	0.2195
R_free r_free	0.2690

Crystal structure of ydcK from Salmonella cholerae at 2.38 A resolution. Northeast Structural Genomics target SCR6

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

Putative transferase

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

2pig__assembly_1__model_1

2pig__assembly_1__model_1 | I(q)

2pig__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

Crystal structure of ydcK from Salmonella cholerae at 2.38 A resolution. Northeast Structural Genomics target SCR6

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

Putative transferase

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

2pig__assembly_1__model_1

2pig__assembly_1__model_1 | I(q)

2pig__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)