SAXSdb — 4g9p

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

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	IRON/SULFUR CLUSTER × 2 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 CHLORIDE ION × 4 POTASSIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPG_THET2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–406； UniProt 1–406

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	4g9p
Deposition date deposition_date	2012-07-24
Structure title title	Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus
Keywords keywords	Oxidoreductase, isoprenoid biosynthesis, non mevalonate pathway, iron-sulphur-cluster, TIM-barrel, MEcPP; OXIDOREDUCTASE
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.

4g9p__assembly_1__model_1

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

Download this curve (.dat)

4g9p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4g9p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.88 Å
Rg (electron density)	28.01 Å
Total Rg	28.69 Å
Atom count	12730
Residues	810
Excluded volume	112980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4g9p__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 (7)

Entity 1 Entity 1 polymer

Description description	4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Molecular weight formula_weight	44281.1 kDa
EC 编号 ec_number	1.17.7.1
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	6938

MEGMRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAGSEIVRLTVNDEEAAKAVPEIKRRLLAEGVEVPLVGDFHFNGHLLLRKYPKMAEALDKFRINPGTLGRGRHKDEHFAEMIRIAMDLGKPVRIGANWGSLDPALLTELMDRNASRPEPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVLSAKVSKARDLVWVYRELARRTQAPLHLGLTEAGMGVKGIVASAAALAPLLLEGIGDTIRVSLTPSPKEPRTKEVEVAQEILQALGLRAFAPEVTSCPGCGRTTSTFFQELAEEVSRRLKERLPEWRARYPGVEELKVAVMGCVVNGPGESKHAHIGISLPGAGEEPKAPVYADGKLLTILKGEGIAEEFLRLVEDYVKTRFAPKA

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	262724
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
Molecular weight formula_weight	278.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	455

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4g9pA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	20 — Dihydropteroate synthase-like

Domain ID domain_id	4g9pA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	413 — Sulfite Reductase Hemoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Sulfite Reductase Hemoprotein, domain 1

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Unit-cell length a length_a	63.650 Å
Unit-cell length b length_b	63.650 Å
Unit-cell length c length_c	442.270 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	46.782 Å
R factor r_factor	0.1779
R_work r_work	0.1767
R_free r_free	0.2025

Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus

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

4-hydroxy-3-methylbut-2-en-1-yl diphosphate 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

4g9p__assembly_1__model_1

4g9p__assembly_1__model_1 | I(q)

4g9p__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus

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

4-hydroxy-3-methylbut-2-en-1-yl diphosphate 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

4g9p__assembly_1__model_1

4g9p__assembly_1__model_1 | I(q)

4g9p__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)