SAXSdb — 1vkf

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

glycerol uptake operon antiterminator-related protein

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	CITRIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PHOSPHATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CITRIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CITRIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1F0_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–188； UniProt 1–176 Author chain B； PDBConstruct 13–188； UniProt 1–176 Author chain C； PDBConstruct 13–188； UniProt 1–176 Author chain D； PDBConstruct 13–188； UniProt 1–176

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	1vkf
Deposition date deposition_date	2004-05-13
Structure title title	CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 A RESOLUTION
Keywords keywords	;GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, 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.

1vkf__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vkf__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vkf__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	16.92 Å
Rg (electron density)	15.68 Å
Total Rg	16.83 Å
Atom count	1303
Residues	168
Excluded volume	23738 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vkf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vkf__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vkf__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1vkf__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	glycerol uptake operon antiterminator-related protein
Molecular weight formula_weight	20973.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5716

MGSDKIHHHHHHMFKGIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVKKAGADGIITIKPKNYVVAKKNGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLPGAVAPKVARKIPGRTVIAAGLVETEEEAREILKHVSAISTSSRILWKMKFLP

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	391

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vkfa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.29 — GlpP-like
Family Family family	c.1.29.1 — GlpP-like

Domain ID domain_id	d1vkfb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.29 — GlpP-like
Family Family family	c.1.29.1 — GlpP-like

Domain ID domain_id	d1vkfc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.29 — GlpP-like
Family Family family	c.1.29.1 — GlpP-like

Domain ID domain_id	d1vkfd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.29 — GlpP-like
Family Family family	c.1.29.1 — GlpP-like

CATH v4.4 (4 domains)

Domain ID domain_id	1vkfA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1vkfB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1vkfC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	1vkfD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	84.527 Å
Unit-cell length b length_b	138.783 Å
Unit-cell length c length_c	160.626 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	72.190 Å
R factor r_factor	0.1865
R_work r_work	0.1852
R_free r_free	0.2113

CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 A RESOLUTION

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

glycerol uptake operon antiterminator-related 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

1vkf__assembly_4__model_1

1vkf__assembly_4__model_1 | I(q)

1vkf__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A GLYCEROL UPTAKE OPERON ANTITERMINATOR-RELATED PROTEIN (TM1436) FROM THERMOTOGA MARITIMA MSB8 AT 1.65 A RESOLUTION

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

glycerol uptake operon antiterminator-related 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

1vkf__assembly_4__model_1

1vkf__assembly_4__model_1 | I(q)

1vkf__assembly_4__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)