2c4u

Crystal structure of the apo form of the 5'-Fluoro-5'-deoxyadenosine synthase enzyme from Streptomyces cattleya

Method: X-RAY DIFFRACTION

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

;5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE ;

STREPTOMYCES CATTLEYA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GLYCEROL × 11 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q70GK9_STRCT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 1–299 Author chain B； PDBConstruct 1–299； UniProt 1–299 Author chain C； PDBConstruct 1–299； UniProt 1–299 Author chain D； PDBConstruct 1–299； UniProt 1–299 Author chain E； PDBConstruct 1–299； UniProt 1–299 Author chain F； PDBConstruct 1–299； UniProt 1–299

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	2c4u
Deposition date deposition_date	2005-10-22
Structure title title	Crystal structure of the apo form of the 5'-Fluoro-5'-deoxyadenosine synthase enzyme from Streptomyces cattleya
Keywords keywords	;TRANSFERASE, FLUORINASE, APO, SAM, FDA, 5'-FLUORODEOXYADANOSINE SYNTHASE ;; 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.

2c4u__assembly_1__model_1

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

Download this curve (.dat)

2c4u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c4u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.30 Å
Rg (electron density)	38.65 Å
Total Rg	39.04 Å
Atom count	13386
Residues	1746
Excluded volume	237330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c4u__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	;5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE ;
Molecular weight formula_weight	32401.5 kDa
EC 编号 ec_number	2.5.1.63
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	13825

MAANSTRRPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEAR

Source Source

Source organism organism	STREPTOMYCES CATTLEYA
NCBI taxonomy ID ncbi_taxonomy_id	29303
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	409

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2c4ua1
Class class	b — All beta proteins
Fold Fold fold	b.141 — Bacterial fluorinating enzyme, C-terminal domain
Superfamily Superfamily superfamily	b.141.1 — Bacterial fluorinating enzyme, C-terminal domain
Family Family family	b.141.1.1 — Bacterial fluorinating enzyme, C-terminal domain

Domain ID domain_id	d2c4ua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.132 — Bacterial fluorinating enzyme, N-terminal domain
Superfamily Superfamily superfamily	c.132.1 — Bacterial fluorinating enzyme, N-terminal domain
Family Family family	c.132.1.1 — Bacterial fluorinating enzyme, N-terminal domain

Domain ID domain_id	d2c4ub1
Class class	b — All beta proteins
Fold Fold fold	b.141 — Bacterial fluorinating enzyme, C-terminal domain
Superfamily Superfamily superfamily	b.141.1 — Bacterial fluorinating enzyme, C-terminal domain
Family Family family	b.141.1.1 — Bacterial fluorinating enzyme, C-terminal domain

Domain ID domain_id	d2c4ub2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.132 — Bacterial fluorinating enzyme, N-terminal domain
Superfamily Superfamily superfamily	c.132.1 — Bacterial fluorinating enzyme, N-terminal domain
Family Family family	c.132.1.1 — Bacterial fluorinating enzyme, N-terminal domain

Domain ID domain_id	d2c4uc1
Class class	b — All beta proteins
Fold Fold fold	b.141 — Bacterial fluorinating enzyme, C-terminal domain
Superfamily Superfamily superfamily	b.141.1 — Bacterial fluorinating enzyme, C-terminal domain
Family Family family	b.141.1.1 — Bacterial fluorinating enzyme, C-terminal domain

Domain ID domain_id	d2c4uc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.132 — Bacterial fluorinating enzyme, N-terminal domain
Superfamily Superfamily superfamily	c.132.1 — Bacterial fluorinating enzyme, N-terminal domain
Family Family family	c.132.1.1 — Bacterial fluorinating enzyme, N-terminal domain

Domain ID domain_id	d2c4ud1
Class class	b — All beta proteins
Fold Fold fold	b.141 — Bacterial fluorinating enzyme, C-terminal domain
Superfamily Superfamily superfamily	b.141.1 — Bacterial fluorinating enzyme, C-terminal domain
Family Family family	b.141.1.1 — Bacterial fluorinating enzyme, C-terminal domain

Domain ID domain_id	d2c4ud2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.132 — Bacterial fluorinating enzyme, N-terminal domain
Superfamily Superfamily superfamily	c.132.1 — Bacterial fluorinating enzyme, N-terminal domain
Family Family family	c.132.1.1 — Bacterial fluorinating enzyme, N-terminal domain

Domain ID domain_id	d2c4ue1
Class class	b — All beta proteins
Fold Fold fold	b.141 — Bacterial fluorinating enzyme, C-terminal domain
Superfamily Superfamily superfamily	b.141.1 — Bacterial fluorinating enzyme, C-terminal domain
Family Family family	b.141.1.1 — Bacterial fluorinating enzyme, C-terminal domain

Domain ID domain_id	d2c4ue2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.132 — Bacterial fluorinating enzyme, N-terminal domain
Superfamily Superfamily superfamily	c.132.1 — Bacterial fluorinating enzyme, N-terminal domain
Family Family family	c.132.1.1 — Bacterial fluorinating enzyme, N-terminal domain

Domain ID domain_id	d2c4uf1
Class class	b — All beta proteins
Fold Fold fold	b.141 — Bacterial fluorinating enzyme, C-terminal domain
Superfamily Superfamily superfamily	b.141.1 — Bacterial fluorinating enzyme, C-terminal domain
Family Family family	b.141.1.1 — Bacterial fluorinating enzyme, C-terminal domain

Domain ID domain_id	d2c4uf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.132 — Bacterial fluorinating enzyme, N-terminal domain
Superfamily Superfamily superfamily	c.132.1 — Bacterial fluorinating enzyme, N-terminal domain
Family Family family	c.132.1.1 — Bacterial fluorinating enzyme, N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	2c4uA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10790 — S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal

Domain ID domain_id	2c4uA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	90 — Bacterial fluorinating enzyme like

Domain ID domain_id	2c4uB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10790 — S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal

Domain ID domain_id	2c4uB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	90 — Bacterial fluorinating enzyme like

Domain ID domain_id	2c4uC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10790 — S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal

Domain ID domain_id	2c4uC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	90 — Bacterial fluorinating enzyme like

Domain ID domain_id	2c4uD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10790 — S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal

Domain ID domain_id	2c4uD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	90 — Bacterial fluorinating enzyme like

Domain ID domain_id	2c4uE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10790 — S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal

Domain ID domain_id	2c4uE02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	90 — Bacterial fluorinating enzyme like

Domain ID domain_id	2c4uF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10790 — S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal

Domain ID domain_id	2c4uF02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	90 — Bacterial fluorinating enzyme like

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Unit-cell length a length_a	103.911 Å
Unit-cell length b length_b	128.064 Å
Unit-cell length c length_c	146.497 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	96.230 Å
R factor r_factor	0.2180
R_work r_work	0.2150
R_free r_free	0.2730

Crystal structure of the apo form of the 5'-Fluoro-5'-deoxyadenosine synthase enzyme from Streptomyces cattleya

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

;5'-FLUORO-5'-DEOXYADENOSINE 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

2c4u__assembly_1__model_1

2c4u__assembly_1__model_1 | I(q)

2c4u__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the apo form of the 5'-Fluoro-5'-deoxyadenosine synthase enzyme from Streptomyces cattleya

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

;5'-FLUORO-5'-DEOXYADENOSINE 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

2c4u__assembly_1__model_1

2c4u__assembly_1__model_1 | I(q)

2c4u__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)