4l7k

Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI)

Method: X-RAY DIFFRACTION

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

Steroid Delta-isomerase

Comamonas testosteroni

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 SULFATE ION × 11 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 SULFATE ION × 8 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 SULFATE ION × 8 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 SULFATE ION × 7 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 SULFATE ION × 10 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDIS_COMTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125 Author chain B； PDBConstruct 1–125； UniProt 1–125 Author chain C； PDBConstruct 1–125； UniProt 1–125 Author chain D； PDBConstruct 1–125； UniProt 1–125 Author chain E； PDBConstruct 1–125； UniProt 1–125 Author chain F； PDBConstruct 1–125； UniProt 1–125 Author chain G； PDBConstruct 1–125； UniProt 1–125 Author chain H； PDBConstruct 1–125； UniProt 1–125 Author chain I； PDBConstruct 1–125； UniProt 1–125 Author chain J； PDBConstruct 1–125； UniProt 1–125 Author chain K； PDBConstruct 1–125； UniProt 1–125 Author chain O； PDBConstruct 1–125； UniProt 1–125

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	4l7k
Deposition date deposition_date	2013-06-14
Structure title title	Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI)
Keywords keywords	Isomerase; ISOMERASE
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.

4l7k__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4l7k__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4l7k__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	19.73 Å
Rg (electron density)	18.50 Å
Total Rg	19.49 Å
Atom count	1928
Residues	248
Excluded volume	33930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4l7k__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4l7k__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4l7k__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4l7k__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4l7k__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4l7k__assembly_6__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 (4)

Entity 1 Entity 1 polymer

Description description	Steroid Delta-isomerase
Molecular weight formula_weight	13426.1 kDa
EC 编号 ec_number	5.3.3.1
Mutation mutation	D38E
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,O
Atom count atom_count	12883

MNTPEHMTAVVQRYVAALNAGDLDGIVALFADDATVEEPVGSEPRSGTAAIREFYANSLKLPLAVELTQEVRAVANEAAFAFTVSFEYQGRKTVVAPIDHFRFNGAGKVVSMRALFGEKNIHAGA

Source Source

Source organism organism	Comamonas testosteroni
NCBI taxonomy ID ncbi_taxonomy_id	285
Host organism host_organism	Escherichia coli

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	5

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	51

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	901

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4l7ka_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kb_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kc_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kd_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7ke_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kf_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kg_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kh_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7ki_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kj_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7kk_
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.17.4.3 — Ketosteroid isomerase-like

Domain ID domain_id	d4l7ko_
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.17.4.3 — Ketosteroid isomerase-like

CATH v4.4 (12 domains)

Domain ID domain_id	4l7kA00
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	4l7kB00
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	4l7kC00
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	4l7kD00
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	4l7kE00
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	4l7kF00
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	4l7kG00
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	4l7kH00
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	4l7kI00
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	4l7kJ00
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	4l7kK00
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	4l7kO00
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	111.128 Å
Unit-cell length b length_b	111.128 Å
Unit-cell length c length_c	499.813 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	144

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.260 Å
R factor r_factor	0.3055
R_work r_work	0.3029
R_free r_free	0.3540

Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI)

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

Steroid Delta-isomerase

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

4l7k__assembly_2__model_1

4l7k__assembly_2__model_1 | I(q)

4l7k__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI)

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

Steroid Delta-isomerase

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

4l7k__assembly_2__model_1

4l7k__assembly_2__model_1 | I(q)

4l7k__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)