SAXSdb — 9c7m

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

Pentalenene synthase

Streptomyces exfoliatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate × 1 MAGNESIUM ION × 3 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	PENA_STREX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–337； UniProt 1–337 Author chain B； PDBConstruct 1–337； UniProt 1–337

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	9c7m
Deposition date deposition_date	2024-06-10
Structure title title	Crystal structure of pentalenene synthase variant F76A complexed with 12,13-difluorofarnesyl diphosphate
Keywords keywords	Terpene synthase, Cyclase, Sesquiterpene synthase, complex, Inhibitor, Fluoro analog, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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.

9c7m__assembly_1__model_1

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

Download this curve (.dat)

9c7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c7m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.09 Å
Rg (electron density)	19.00 Å
Total Rg	19.89 Å
Atom count	2516
Residues	318
Excluded volume	43989 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c7m__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9c7m__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 (4)

Entity 1 Entity 1 polymer

Description description	Pentalenene synthase
Molecular weight formula_weight	37974.3 kDa
EC 编号 ec_number	4.2.3.7
Mutation mutation	F76A
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	5010

MPQDVDFHIPLPGRQSPDHARAEAEQLAWPRSLGLIRSDAAAERHLRGGYADLASRFYPHATGADLDLGVDLMSWAFLFDDLFDGPRGENPEDTKQLTDQVAAALDGPLPDTAPPIAHGFADIWRRTCEGMTPAWCARSARHWRNYFDGYVDEAESRFWNAPCDSAAQYLAMRRHTIGVQPTVDLAERAGRFEVPHRVFDSAVMSAMLQIAVDVNLLLNDIASLEKEEARGEQNNMVMILRREHGWSKSRSVSHMQNEVRARLEQYLLLESCLPKVGEIYQLDTAEREALERYRTDAVRTVIRGSYDWHRSSGRYDAEFALAAGAQGYLEELGSSAH

Source Source

Source organism organism	Streptomyces exfoliatus
NCBI taxonomy ID ncbi_taxonomy_id	1905
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
Molecular weight formula_weight	418.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

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Unit-cell length a length_a	180.530 Å
Unit-cell length b length_b	180.530 Å
Unit-cell length c length_c	55.861 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	hexagonal

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.1997
R_work r_work	0.1982
R_free r_free	0.2298

Crystal structure of pentalenene synthase variant F76A complexed with 12,13-difluorofarnesyl diphosphate

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

Pentalenene 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

9c7m__assembly_1__model_1

9c7m__assembly_1__model_1 | I(q)

9c7m__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

7. Citations (1)

Crystal structure of pentalenene synthase variant F76A complexed with 12,13-difluorofarnesyl diphosphate

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

Pentalenene 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

9c7m__assembly_1__model_1

9c7m__assembly_1__model_1 | I(q)

9c7m__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

7. Citations (1)