SAXSdb — 2vzm

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

CYTOCHROME P450 MONOOXYGENASE

STREPTOMYCES VENEZUELAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 NARBOMYCIN × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 NARBOMYCIN × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87605_9ACTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–436； UniProt 1–416 Author chain B； PDBConstruct 21–436； UniProt 1–416

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	2vzm
Deposition date deposition_date	2008-08-01
Structure title title	Crystal structure of the narbomycin-bound PikC D50N mutant
Keywords keywords	;OXIDOREDUCTASE, PIKC, IRON, HEME, CYP107L1, MONOOXYGENASE, ANTIBIOTIC BIOSYNTHESIS, MACROLIDE MONOOXYGENASE, METAL-BINDING, CYTOCHROME P450 ;; 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.

2vzm__assembly_1__model_1

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

Download this curve (.dat)

2vzm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vzm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.06 Å
Rg (electron density)	20.64 Å
Total Rg	21.49 Å
Atom count	3141
Residues	395
Excluded volume	55853 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vzm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vzm__assembly_2__model_1`	monomeric （1）	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	CYTOCHROME P450 MONOOXYGENASE
Molecular weight formula_weight	48267.8 kDa
Mutation mutation	YES
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	7068

MGSSHHHHHHSSGLVPRGSHMRRTQQGTTASPPVLDLGALGQDFAADPYPTYARLRAEGPAHRVRTPEGNEVWLVVGYDRARAVLADPRFSKDWRNSTTPLTEAEAALNHNMLESDPPRHTRLRKLVAREFTMRRVELLRPRVQEIVDGLVDAMLAAPDGRADLMESLAWPLPITVISELLGVPEPDRAAFRVWTDAFVFPDDPAQAQTAMAEMSGYLSRLIDSKRGQDGEDLLSALVRTSDEDGSRLTSEELLGMAHILLVAGHETTVNLIANGMYALLSHPDQLAALRADMTLLDGAVEEMLRYEGPVESATYRFPVEPVDLDGTVIPAGDTVLVVLADAHRTPERFPDPHRFDIRRDTAGHLAFGHGIHFCIGAPLARLEARIAVRALLERCPDLALDVSPGELVWYPNPMIRGLKALPIRWRRGREAGRRTG

Source Source

Source organism organism	STREPTOMYCES VENEZUELAE
NCBI taxonomy ID ncbi_taxonomy_id	54571
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NARBOMYCIN
Molecular weight formula_weight	509.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	641

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vzma_
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	d2vzmb_
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

CATH v4.4 (2 domains)

Domain ID domain_id	2vzmA00
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	2vzmB00
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	60.358 Å
Unit-cell length b length_b	109.489 Å
Unit-cell length c length_c	153.096 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	1.850 Å
Low-resolution limit resolution_low	89.090 Å
R factor r_factor	0.1697
R_work r_work	0.1651
R_free r_free	0.2108

Crystal structure of the narbomycin-bound PikC D50N mutant

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

CYTOCHROME P450 MONOOXYGENASE

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

2vzm__assembly_1__model_1

2vzm__assembly_1__model_1 | I(q)

2vzm__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the narbomycin-bound PikC D50N mutant

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

CYTOCHROME P450 MONOOXYGENASE

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

2vzm__assembly_1__model_1

2vzm__assembly_1__model_1 | I(q)

2vzm__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)