SAXSdb — 5gkw

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

Limonene-1,2-epoxide hydrolase

Rhodococcus erythropolis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(1~{R},2~{R})-cyclopentane-1,2-diol × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	(1~{R},2~{R})-cyclopentane-1,2-diol × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIMA_RHOER
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–155； UniProt 2–149 Author chain B； PDBConstruct 8–155； UniProt 2–149

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	5gkw
Deposition date deposition_date	2016-07-07
Structure title title	crystal structure of SZ529 complex with (R,R)-cyclopentanediol
Keywords keywords	mutant R, R-selectivity, 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.

5gkw__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5gkw__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5gkw__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.97 Å
Rg (electron density)	17.86 Å
Total Rg	18.92 Å
Atom count	1766
Residues	230
Excluded volume	31346 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5gkw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5gkw__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5gkw__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5gkw__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	Limonene-1,2-epoxide hydrolase
Molecular weight formula_weight	17319.3 kDa
EC 编号 ec_number	3.3.2.8
Mutation mutation	M32V/M78V/I80V/L114F
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	2166

MHHHHHHTSKIEQPRWASKDSAAGAASTPDEKIVLEFVDALTSNDAAKLIEYFAEDTMYQNMPLPPAYGRDAVEQTLAGLFTVVSVDAVETFHIGSSNGLVYTERVDVLRALPTGKSYNFSILGVFQLTEGKITGWRDYFDLREFEEAVDLPLRG

Source Source

Source organism organism	Rhodococcus erythropolis
NCBI taxonomy ID ncbi_taxonomy_id	1833
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(1~{R},2~{R})-cyclopentane-1,2-diol
Molecular weight formula_weight	102.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	144

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5gkwa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.8 — Limonene-1,2-epoxide hydrolase-like

Domain ID domain_id	d5gkwb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.8 — Limonene-1,2-epoxide hydrolase-like

CATH v4.4 (2 domains)

Domain ID domain_id	5gkwA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5gkwB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	51.856 Å
Unit-cell length b length_b	60.541 Å
Unit-cell length c length_c	119.272 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.010 Å
Low-resolution limit resolution_low	47.556 Å
R factor r_factor	0.2280
R_work r_work	0.2261
R_free r_free	0.2634

crystal structure of SZ529 complex with (R,R)-cyclopentanediol

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

Limonene-1,2-epoxide hydrolase

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

5gkw__assembly_4__model_1

5gkw__assembly_4__model_1 | I(q)

5gkw__assembly_4__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

crystal structure of SZ529 complex with (R,R)-cyclopentanediol

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

Limonene-1,2-epoxide hydrolase

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

5gkw__assembly_4__model_1

5gkw__assembly_4__model_1 | I(q)

5gkw__assembly_4__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)