SAXSdb — 2f6x

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

(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SN-GLYCEROL-1-PHOSPHATE × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCRB_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–234； UniProt 1–231 Author chain B； PDBConstruct 4–234； UniProt 1–231

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	2f6x
Deposition date deposition_date	2005-11-29
Structure title title	Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase complexed with sn-G1P and MPD
Keywords keywords	;non-canonical TIM-barrel; prenyltransferase; archaeal lipid synthesis; sn-glycerol-1-phosphate; 2-methyl-2, 4-pentanediol; dimer, 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.

2f6x__assembly_1__model_1

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

Download this curve (.dat)

2f6x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f6x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.33 Å
Rg (electron density)	24.29 Å
Total Rg	25.16 Å
Atom count	3725
Residues	462
Excluded volume	66805 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f6x__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 (4)

Entity 1 Entity 1 polymer

Description description	(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase
Molecular weight formula_weight	26455.1 kDa
EC 编号 ec_number	2.5.1.42
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	4025

GSHMRWRKWRHITKLDPDRTNTDEIIKAVADSGTDAVMISGTQNVTYEKARTLIEKVSQYGLPIVVEPSDPSNVVYDVDYLFVPTVLNSADGDWITGKHAQWVRMHYENLQKFTEIIESEFIQIEGYIVLNPDSAVARVTKALCNIDKELAASYALVGEKLFNLPIIYIEYSGTYGNPELVAEVKKVLDKARLFYGGGIDSREKAREMLRYADTIIVGNVIYEKGIDAFLETLP

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SN-GLYCEROL-1-PHOSPHATE
Molecular weight formula_weight	172.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	222

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2f6xa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d2f6xb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

CATH v4.4 (2 domains)

Domain ID domain_id	2f6xA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	390 — FMN-linked oxidoreductases

Domain ID domain_id	2f6xB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	390 — FMN-linked oxidoreductases

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Unit-cell length a length_a	95.880 Å
Unit-cell length b length_b	95.880 Å
Unit-cell length c length_c	166.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1879
R_free r_free	0.2274

Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase complexed with sn-G1P and MPD

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

(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase

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

2f6x__assembly_1__model_1

2f6x__assembly_1__model_1 | I(q)

2f6x__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase complexed with sn-G1P and MPD

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

(S)-3-O-Geranylgeranylglyceryl Phosphate Synthase

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

2f6x__assembly_1__model_1

2f6x__assembly_1__model_1 | I(q)

2f6x__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)