9wma

Crystal structure of a P450 BM3 heme domain mutant

Method: X-RAY DIFFRACTION

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

Bifunctional cytochrome P450/NADPH--P450 reductase

Priestia megaterium (strain NBRC 15308)

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 IMIDAZOLE × 1 DI(HYDROXYETHYL)ETHER × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 IMIDAZOLE × 1 DI(HYDROXYETHYL)ETHER × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CHLORIDE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPXB_PRIM2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–455； UniProt 2–456 Author chain B； PDBConstruct 1–455； UniProt 2–456

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	9wma
Deposition date deposition_date	2025-09-03
Last revision last_revision	2026-03-18
Structure title title	Crystal structure of a P450 BM3 heme domain mutant
Keywords keywords	P450, Metal-binding, Heme, OXIDOREDUCTASE; 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.

9wma__assembly_1__model_1

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

Download this curve (.dat)

9wma__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9wma__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.32 Å
Rg (electron density)	21.96 Å
Total Rg	22.89 Å
Atom count	3712
Residues	452
Excluded volume	66217 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9wma__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9wma__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 (7)

Entity 1 Entity 1 polymer

Description description	Bifunctional cytochrome P450/NADPH--P450 reductase
Molecular weight formula_weight	52146.3 kDa
EC 编号 ec_number	1.14.14.1,1.6.2.4
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	8826

AIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGWVTRYLSSQRLIKEACDESRFDKNLWQALNFLREIQGDGLGLSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSTVRALDEAQNKLQRANPDDPAYDENKRQIQEDTKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL

Source Source

Source organism organism	Priestia megaterium (strain NBRC 15308)
Common name common_name	Bacillus megaterium
NCBI taxonomy ID ncbi_taxonomy_id	1348623
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	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1203

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Unit-cell length a length_a	58.950 Å
Unit-cell length b length_b	146.841 Å
Unit-cell length c length_c	63.383 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.570 Å
Low-resolution limit resolution_low	24.750 Å
R factor r_factor	0.1475
R_work r_work	0.1458
R_free r_free	0.1788

Crystal structure of a P450 BM3 heme domain mutant

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

Bifunctional cytochrome P450/NADPH--P450 reductase

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

9wma__assembly_1__model_1

9wma__assembly_1__model_1 | I(q)

9wma__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of a P450 BM3 heme domain mutant

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

Bifunctional cytochrome P450/NADPH--P450 reductase

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

9wma__assembly_1__model_1

9wma__assembly_1__model_1 | I(q)

9wma__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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)