SAXSdb — 3npl

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

Bifunctional P-450/NADPH-P450 reductase

Bacillus megaterium

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 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[2-iodo-N-(1,10-phenanthrolin-5-yl-kappa~2~N~1~,N~10~)acetamide]ruthenium(2+) × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPXB_BACME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–464； UniProt 1–464 Author chain B； PDBConstruct 1–464； UniProt 1–464

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	3npl
Deposition date deposition_date	2010-06-28
Structure title title	Structure of Ru(bpy)2(A-Phen)(K97C) P450 BM3 heme domain, a ruthenium modified P450 BM3 mutant
Keywords keywords	P450 BM3 heme domain, mutant proteins, electron transfer, 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.

3npl__assembly_1__model_1

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

Download this curve (.dat)

3npl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3npl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.42 Å
Rg (electron density)	22.02 Å
Total Rg	22.95 Å
Atom count	3710
Residues	456
Excluded volume	66168 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3npl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3npl__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 (5)

Entity 1 Entity 1 polymer

Description description	Bifunctional P-450/NADPH-P450 reductase
Molecular weight formula_weight	53752.1 kDa
EC 编号 ec_number	1.14.14.1
Mutation mutation	C62A, K97C, C156S
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	7936

MTIKEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEAADESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWCKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLSGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGIPSPSTHHHHHH

Source Source

Source organism organism	Bacillus megaterium
NCBI taxonomy ID ncbi_taxonomy_id	1404
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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[2-iodo-N-(1,10-phenanthrolin-5-yl-kappa~2~N~1~,N~10~)acetamide]ruthenium(2+)
Molecular weight formula_weight	776.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	436

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3npla_
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.104.1.1 — Cytochrome P450

Domain ID domain_id	d3nplb_
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.104.1.1 — Cytochrome P450

CATH v4.4 (2 domains)

Domain ID domain_id	3nplA00
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	3nplB00
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	117.078 Å
Unit-cell length b length_b	117.078 Å
Unit-cell length c length_c	273.850 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2027
R_work r_work	0.2008
R_free r_free	0.2382

Structure of Ru(bpy)2(A-Phen)(K97C) P450 BM3 heme domain, a ruthenium modified P450 BM3 mutant

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

Bifunctional P-450/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

3npl__assembly_1__model_1

3npl__assembly_1__model_1 | I(q)

3npl__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Ru(bpy)2(A-Phen)(K97C) P450 BM3 heme domain, a ruthenium modified P450 BM3 mutant

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

Bifunctional P-450/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

3npl__assembly_1__model_1

3npl__assembly_1__model_1 | I(q)

3npl__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)