SAXSdb — 2b8n

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

glycerate kinase, putative

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1S1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–429； UniProt 1–417 Author chain B； PDBConstruct 13–429； UniProt 1–417

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	2b8n
Deposition date deposition_date	2005-10-07
Structure title title	Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at 2.70 A resolution
Keywords keywords	;tm1585, Glycerate kinase (EC 2.7.1.31), Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, 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.

2b8n__assembly_1__model_1

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

Download this curve (.dat)

2b8n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b8n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.43 Å
Rg (electron density)	23.65 Å
Total Rg	24.50 Å
Atom count	3085
Residues	411
Excluded volume	55569 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b8n__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2b8n__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Description description	glycerate kinase, putative
Molecular weight formula_weight	46476.4 kDa
EC 编号 ec_number	2.7.1.31
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	6244

MGSDKIHHHHHHMFDPESLKKLAIEIVKKSIEAVFPDRAVKETLPKLNLDRVILVAVGKAAWRMAKAAYEVLGKKIRKGVVVTKYGHSEGPIDDFEIYEAGHPVPDENTIKTTRRVLELVDQLNENDTVLFLLSGGGSSLFELPLEGVSLEEIQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIASGPAWPDSSTSEDALKVLEKYGIETSESVKRAILQETPKHLSNVEIHLIGNVQKVCDEAKSLAKEKGFNAEIITTSLDCEAREAGRFIASIMKEVKFKDRPLKKPAALIFGGETVVHVKGNGIGGRNQELALSAAIALEGIEGVILCSAGTDGTDGPTDAAGGIVDGSTAKTLKAMGEDPYQYLKNNDSYNALKKSGALLITGPTGTNVNDLIIGLIV

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2b8na_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.118 — GckA/TtuD-like
Superfamily Superfamily superfamily	c.118.1 — GckA/TtuD-like
Family Family family	c.118.1.1 — GckA/TtuD-like

Domain ID domain_id	d2b8nb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.118 — GckA/TtuD-like
Superfamily Superfamily superfamily	c.118.1 — GckA/TtuD-like
Family Family family	c.118.1.1 — GckA/TtuD-like

CATH v4.4 (4 domains)

Domain ID domain_id	2b8nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1480 — glycerate kinase, domain 1
Homologous superfamily homologous superfamily	10 — MOFRL domain

Domain ID domain_id	2b8nA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10180 — Glycerate kinase, MOFRL-like N-terminal domain

Domain ID domain_id	2b8nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1480 — glycerate kinase, domain 1
Homologous superfamily homologous superfamily	10 — MOFRL domain

Domain ID domain_id	2b8nB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10180 — Glycerate kinase, MOFRL-like N-terminal domain

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Unit-cell length a length_a	61.954 Å
Unit-cell length b length_b	85.169 Å
Unit-cell length c length_c	172.507 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	2.530 Å
Low-resolution limit resolution_low	48.110 Å
R factor r_factor	0.1848
R_work r_work	0.1820
R_free r_free	0.2460

Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at 2.70 A resolution

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

glycerate kinase, putative

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

2b8n__assembly_1__model_1

2b8n__assembly_1__model_1 | I(q)

2b8n__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at 2.70 A resolution

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

glycerate kinase, putative

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

2b8n__assembly_1__model_1

2b8n__assembly_1__model_1 | I(q)

2b8n__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)