3zby

Ligand-free structure of CYP142 from Mycobacterium smegmatis

Method: X-RAY DIFFRACTION

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

P450 HEME-THIOLATE PROTEIN

Mycobacterium smegmatis str. MC2 155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 SULFATE ION × 6 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 SULFATE ION × 6 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
3	Other combination	Homooligomer	Protein 2 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 SULFATE ION × 4 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
4	Other combination	Homooligomer	Protein 2 其他Polymer 2	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 PROTOPORPHYRIN IX CONTAINING FE × 2 SULFATE ION × 6 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0R4Q6_MYCS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 1–401 Author chain B； PDBConstruct 1–401； UniProt 1–401 Author chain C； PDBConstruct 1–401； UniProt 1–401 Author chain D； PDBConstruct 1–401； UniProt 1–401 Author chain E； PDBConstruct 1–401； UniProt 1–401 Author chain F； PDBConstruct 1–401； UniProt 1–401

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	3zby
Deposition date deposition_date	2012-11-13
Structure title title	Ligand-free structure of CYP142 from Mycobacterium smegmatis
Keywords keywords	OXIDOREDUCTASE, CYP142, CHOLESTEROL METABOLISM; OXIDOREDUCTASE
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.

3zby__assembly_1__model_1

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

Download this curve (.dat)

3zby__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zby__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.99 Å
Rg (electron density)	33.09 Å
Total Rg	33.60 Å
Atom count	6553
Residues	804
Excluded volume	115990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zby__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zby__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3zby__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3zby__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 (6)

Entity 1 Entity 1 polymer

Description description	P450 HEME-THIOLATE PROTEIN
Molecular weight formula_weight	45780.0 kDa
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	22588

MTQMLTRPDVDLVNGMFYADGGAREAYRWMRANEPVFRDRNGLAAATTYQAVLDAERNPELFSSTGGIRPDQPGMPYMIDMDDPQHLLRRKLVNAGFTRKRVMDKVDSIGRLCDTLIDAVCERGECDFVRDIAAPLPMAVIGDMLGVLPTERDMLLKWSDDLVCGLSSHVDEAAIQKLMDTFAAYTEFTKDVITKRRAEPTDDLFSVLVNSEVEGQRMSDDEIVFETLLILIGGDETTRHTLSGGTEQLLRHRDQWDALVADVDLLPGAIEEMLRWTSPVKNMCRTLTADTVFHGTELRAGEKIMLMFESANFDESVFGDPDNFRIDRNPNSHVAFGFGTHFCLGNQLARLELRLMTERVLRRLPDLRLADDAPVPLRPANFVSGPESMPVVFTPSAPVLAHHHHHH

Source Source

Source organism organism	Mycobacterium smegmatis str. MC2 155
NCBI taxonomy ID ncbi_taxonomy_id	246196
Host organism host_organism	Escherichia coli DH5[alpha]

Entity 2 Entity 2 branched

Description description	Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
Molecular weight formula_weight	1153.0 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2637

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3zbya1
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3zbya2
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	d3zbyb1
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3zbyb2
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	d3zbyc1
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3zbyc2
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	d3zbyd1
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3zbyd2
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	d3zbye1
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3zbye2
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	d3zbyf1
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3zbyf2
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 (6 domains)

Domain ID domain_id	3zbyA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3zbyB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3zbyC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3zbyD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3zbyE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3zbyF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

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Unit-cell length a length_a	94.051 Å
Unit-cell length b length_b	162.847 Å
Unit-cell length c length_c	266.443 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	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	266.440 Å
R factor r_factor	0.1918
R_work r_work	0.1898
R_free r_free	0.2298

Ligand-free structure of CYP142 from Mycobacterium smegmatis

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

P450 HEME-THIOLATE PROTEIN

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

3zby__assembly_1__model_1

3zby__assembly_1__model_1 | I(q)

3zby__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Ligand-free structure of CYP142 from Mycobacterium smegmatis

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

P450 HEME-THIOLATE PROTEIN

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

3zby__assembly_1__model_1

3zby__assembly_1__model_1 | I(q)

3zby__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)