SAXSdb — 5gnl

▼

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

Vitamin D(3) 25-hydroxylase

Pseudonocardia autotrophica

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 2-(2-METHOXYETHOXY)ETHANOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPVDH_PSEAH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–403； UniProt 1–403

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5gnl
Deposition date deposition_date	2016-07-22
Structure title title	Cytochrome P450 Vdh (CYP107BR1) F106V mutant
Keywords keywords	OXIDOREDUCTASE, cytochrome P450; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5gnl__assembly_1__model_1

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

Download this curve (.dat)

5gnl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5gnl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.61 Å
Rg (electron density)	21.16 Å
Total Rg	22.01 Å
Atom count	3109
Residues	395
Excluded volume	55233 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5gnl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vitamin D(3) 25-hydroxylase
Molecular weight formula_weight	45439.6 kDa
EC 编号 ec_number	1.14.15.15
Mutation mutation	F106V
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3226

MALTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSVTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCLGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPRSALEHHHHHH

Source Source

Source organism organism	Pseudonocardia autotrophica
Common name common_name	Amycolata autotrophica
NCBI taxonomy ID ncbi_taxonomy_id	2074
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	1

Entity 3 Entity 3 non-polymer

Description description	2-(2-METHOXYETHOXY)ETHANOL
Molecular weight formula_weight	120.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5gnla_
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 (1 domains)

Domain ID domain_id	5gnlA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

▶

Unit-cell length a length_a	61.670 Å
Unit-cell length b length_b	61.670 Å
Unit-cell length c length_c	98.166 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	3

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2013
R_work r_work	0.1996
R_free r_free	0.2342

Cytochrome P450 Vdh (CYP107BR1) F106V mutant

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

Vitamin D(3) 25-hydroxylase

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

5gnl__assembly_1__model_1

5gnl__assembly_1__model_1 | I(q)

5gnl__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Cytochrome P450 Vdh (CYP107BR1) F106V mutant

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

Vitamin D(3) 25-hydroxylase

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

5gnl__assembly_1__model_1

5gnl__assembly_1__model_1 | I(q)

5gnl__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)