SAXSdb — 3f7w

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

putative fructosamine-3-kinase

Thermobifida fusca YX

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	UNKNOWN LIGAND × 1 CHLORIDE ION × 2 1,2-ETHANEDIOL × 5 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q47ME9_THEFY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–288； UniProt 2–287

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	3f7w
Deposition date deposition_date	2008-11-10
Structure title title	Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution
Keywords keywords	;YP_290396.1, putative fructosamine-3-kinase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Unknown function, 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.

3f7w__assembly_1__model_1

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

Download this curve (.dat)

3f7w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f7w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.33 Å
Rg (electron density)	19.24 Å
Total Rg	20.09 Å
Atom count	2265
Residues	284
Excluded volume	39909 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f7w__assembly_1__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	putative fructosamine-3-kinase
Molecular weight formula_weight	31804.2 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	2752

GVNSVAARVTELTGREVAAVAERGHSHRWHLYRVELADGTPLFVKALPDDAPALDGLFRAEALGLDWLGRSFGSPVPQVAGWDDRTLAMEWVDERPPTPEAAERFGHQLAAMHLAGAESFGATWDGYIGPLPMDNTPRSTWPEFYAEQRILPYLRRAADRGALTPGDVRLVEKVLDALDHLAGDPEPPARIHGDLWNGNVLWQDDGAVVIDPAAHGGHREADLAMLALFGLPYLDRVRDAYNEVAPLAEGWRARIPLHQLHPLLVHVCLFGAAYRTTLVDTARAALRA

Source Source

Source organism organism	Thermobifida fusca YX
NCBI taxonomy ID ncbi_taxonomy_id	269800
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	323

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3f7wA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3f7wA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	3f7wA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	240 —

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Unit-cell length a length_a	91.178 Å
Unit-cell length b length_b	91.178 Å
Unit-cell length c length_c	82.049 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	28.916 Å
R factor r_factor	0.1670
R_work r_work	0.1650
R_free r_free	0.2040

Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution

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

putative fructosamine-3-kinase

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

3f7w__assembly_1__model_1

3f7w__assembly_1__model_1 | I(q)

3f7w__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of putative fructosamine-3-kinase (YP_290396.1) from THERMOBIFIDA FUSCA YX-ER1 at 1.85 A resolution

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

putative fructosamine-3-kinase

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

3f7w__assembly_1__model_1

3f7w__assembly_1__model_1 | I(q)

3f7w__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)