SAXSdb — 4r9l

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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 homooligomer	Homooligomer	Protein 2	(2R)-2-hydroxyhexanamide × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	(2R)-2-hydroxyhexanamide × 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 3–149； UniProt 3–149 Author chain B； PDBConstruct 3–149； UniProt 3–149 Author chain C； PDBConstruct 3–149； UniProt 3–149

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	4r9l
Deposition date deposition_date	2014-09-05
Structure title title	Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis, containing two stabilizing disulfide bonds
Keywords keywords	limonene epoxide hydrolase, NTF-2 fold, engineered, thermostable, 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.

4r9l__assembly_1__model_1

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

Download this curve (.dat)

4r9l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4r9l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.57 Å
Rg (electron density)	18.33 Å
Total Rg	19.37 Å
Atom count	2367
Residues	300
Excluded volume	42443 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4r9l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4r9l__assembly_2__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	19508.2 kDa
EC 编号 ec_number	3.3.2.8
Mutation mutation	I5C, S15P, A19K, T76K, E84C, T85V, G89C, S91C, N92K, Y96F, E124D
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3854

MASKCEQPRWASKDPAAGKASTPDEKIVLEFMDALTSNDAAKLIEYFAEDTMYQNMPLPPAYGRDAVEQTLAGLFKVMSIDAVCVFHICSCKGLVFTERVDVLRALPTGKSYNLSILGVFQLTDGKITGWRDYFDLREFEEAVDLPLRGKLGPEQKLISEEDLNSAVDHHHHHH

Source Source

Source organism organism	Rhodococcus erythropolis
NCBI taxonomy ID ncbi_taxonomy_id	1833
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2R)-2-hydroxyhexanamide
Molecular weight formula_weight	131.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4r9la1
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	d4r9la2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4r9lb1
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	d4r9lb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4r9lc1
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	d4r9lc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	4r9lA00
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	4r9lB00
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	4r9lC00
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	87.688 Å
Unit-cell length b length_b	87.688 Å
Unit-cell length c length_c	108.905 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	44.250 Å
R factor r_factor	0.1627
R_work r_work	0.1604
R_free r_free	0.2068

Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis, containing two stabilizing disulfide bonds

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

4r9l__assembly_1__model_1

4r9l__assembly_1__model_1 | I(q)

4r9l__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) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis, containing two stabilizing disulfide bonds

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

4r9l__assembly_1__model_1

4r9l__assembly_1__model_1 | I(q)

4r9l__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) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. Citations (1)