9rp2

Ensemble refined structure of CotB2 F107A in complex with alendronate

Method: X-RAY DIFFRACTION

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

Cyclooctat-9-en-7-ol synthase

Streptomyces melanosporofaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(4S)-2-METHYL-2,4-PENTANEDIOL × 4 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE × 2 MAGNESIUM ION × 6 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COTB2_STRMJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–307； UniProt 1–307 Author chain B； PDBConstruct 1–307； UniProt 1–307

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	9rp2
Deposition date deposition_date	2025-06-23
Structure title title	Ensemble refined structure of CotB2 F107A in complex with alendronate
Keywords keywords	TERPENE SYNTHASE, CYCLOOCTATIN, DITERPENCE SYNTHASE, HYDROLASE; HYDROLASE
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.

9rp2__assembly_1__model_36

Assembly 1 · Model 36 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9rp2__assembly_1__model_36 | I(q)

100 plotted points; both axes use logarithmic scales.

9rp2__assembly_1__model_36 | P(r) · Pending

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

Rg（Guinier）	25.16 Å
Rg (electron density)	24.11 Å
Total Rg	25.01 Å
Atom count	4885
Residues	591
Excluded volume	86624 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rp2__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`9rp2__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`9rp2__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`9rp2__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`9rp2__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`9rp2__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`9rp2__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`9rp2__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`9rp2__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`9rp2__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`9rp2__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`9rp2__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`9rp2__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`9rp2__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`9rp2__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`9rp2__assembly_1__model_16`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`9rp2__assembly_1__model_17`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`9rp2__assembly_1__model_18`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`9rp2__assembly_1__model_19`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`9rp2__assembly_1__model_20`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	21	`9rp2__assembly_1__model_21`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	22	`9rp2__assembly_1__model_22`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	23	`9rp2__assembly_1__model_23`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	24	`9rp2__assembly_1__model_24`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	25	`9rp2__assembly_1__model_25`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	26	`9rp2__assembly_1__model_26`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	27	`9rp2__assembly_1__model_27`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	28	`9rp2__assembly_1__model_28`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	29	`9rp2__assembly_1__model_29`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	30	`9rp2__assembly_1__model_30`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	31	`9rp2__assembly_1__model_31`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	32	`9rp2__assembly_1__model_32`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	33	`9rp2__assembly_1__model_33`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	34	`9rp2__assembly_1__model_34`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	35	`9rp2__assembly_1__model_35`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	36	`9rp2__assembly_1__model_36`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	37	`9rp2__assembly_1__model_37`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	38	`9rp2__assembly_1__model_38`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	39	`9rp2__assembly_1__model_39`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	40	`9rp2__assembly_1__model_40`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	41	`9rp2__assembly_1__model_41`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	42	`9rp2__assembly_1__model_42`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	43	`9rp2__assembly_1__model_43`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	44	`9rp2__assembly_1__model_44`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	45	`9rp2__assembly_1__model_45`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	46	`9rp2__assembly_1__model_46`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	47	`9rp2__assembly_1__model_47`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	48	`9rp2__assembly_1__model_48`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	49	`9rp2__assembly_1__model_49`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	50	`9rp2__assembly_1__model_50`	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 (6)

Entity 1 Entity 1 polymer

Description description	Cyclooctat-9-en-7-ol synthase
Molecular weight formula_weight	36694.4 kDa
EC 编号 ec_number	4.2.3.146
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	261865

MTTGLSTAGAQDIGRSSVRPYLEECTRRFQEMFDRHVVTRPTKVELTDAELREVIDDCNAAVAPLGKTVSDERWISYVGVVLWSQSPRHIKDMEAFKAVCVLNCVTAVWDDMDPALHDFGLFLPQLRKICEKYYGPEDAEVAYEAARAFVTSDHMFRDSPIKAALCTTSPEQYFRFRVTDIGVDFWMKMSYPIYRHPEFTEHAKTSLAARMTTRGLTIVNDFYSYDREVSLGQITNCFRLCDVSDETAFKEFFQARLDDMIEDIECIKAFDQLTQDVFLDLIYGNFVWTTSNKRYKTAVNDVNSRIQAAALEHHHHHH

Source Source

Source organism organism	Streptomyces melanosporofaciens
NCBI taxonomy ID ncbi_taxonomy_id	67327
Host organism host_organism	Escherichia coli DH5[alpha]

Entity 2 Entity 2 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	4

Entity 3 Entity 3 non-polymer

Description description	4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE
Molecular weight formula_weight	245.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	353

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Unit-cell length a length_a	62.811 Å
Unit-cell length b length_b	98.050 Å
Unit-cell length c length_c	106.830 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	1.930 Å
Low-resolution limit resolution_low	16.480 Å
R factor r_factor	0.1810
R_work r_work	0.1795
R_free r_free	0.2163

Ensemble refined structure of CotB2 F107A in complex with alendronate

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

Cyclooctat-9-en-7-ol 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

9rp2__assembly_1__model_36

9rp2__assembly_1__model_36 | I(q)

9rp2__assembly_1__model_36 | 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 (6)

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 water

7. Citations (2)

Ensemble refined structure of CotB2 F107A in complex with alendronate

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

Cyclooctat-9-en-7-ol 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

9rp2__assembly_1__model_36

9rp2__assembly_1__model_36 | I(q)

9rp2__assembly_1__model_36 | 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 (6)

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 water

7. Citations (2)