SAXSdb — 1n23

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

(+)-bornyl diphosphate synthase

Salvia officinalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 6 (1R,4S)-2-AZABORNANE × 2 PYROPHOSPHATE 2- × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BPPS_SALOF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–549； UniProt 50–598 Author chain B； PDBConstruct 1–549； UniProt 50–598

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	1n23
Deposition date deposition_date	2002-10-21
Structure title title	(+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, and (1R,4S)-2-azabornane
Keywords keywords	terpene synthase fold, isomerase; ISOMERASE
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.

1n23__assembly_1__model_1

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

Download this curve (.dat)

1n23__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n23__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.64 Å
Rg (electron density)	36.47 Å
Total Rg	37.00 Å
Atom count	8786
Residues	1060
Excluded volume	156880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n23__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 (5)

Entity 1 Entity 1 polymer

Description description	(+)-bornyl diphosphate synthase
Molecular weight formula_weight	64035.7 kDa
EC 编号 ec_number	5.5.1.8
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	9008

EAHQIRRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDEGGNEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA

Source Source

Source organism organism	Salvia officinalis
Common name common_name	garden sage
NCBI taxonomy ID ncbi_taxonomy_id	38868
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	(1R,4S)-2-AZABORNANE
Molecular weight formula_weight	139.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1n23a1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.1 — Terpenoid cyclase N-terminal domain

Domain ID domain_id	d1n23a2
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.3 — Terpenoid cyclase C-terminal domain

Domain ID domain_id	d1n23b1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.1 — Terpenoid cyclase N-terminal domain

Domain ID domain_id	d1n23b2
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.3 — Terpenoid cyclase C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1n23A01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	130 — Terpene synthase, N-terminal domain

Domain ID domain_id	1n23A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	1n23B01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	130 — Terpene synthase, N-terminal domain

Domain ID domain_id	1n23B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

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Unit-cell length a length_a	100.990 Å
Unit-cell length b length_b	118.180 Å
Unit-cell length c length_c	120.070 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	2.400 Å
Low-resolution limit resolution_low	29.360 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2440

(+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, and (1R,4S)-2-azabornane

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

(+)-bornyl 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

1n23__assembly_1__model_1

1n23__assembly_1__model_1 | I(q)

1n23__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

(+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, and (1R,4S)-2-azabornane

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

(+)-bornyl 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

1n23__assembly_1__model_1

1n23__assembly_1__model_1 | I(q)

1n23__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)