SAXSdb — 3vzx

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

Heptaprenylglyceryl phosphate synthase

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 10 CHLORIDE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCRB_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 1–228 Author chain B； PDBConstruct 1–228； UniProt 1–228

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	3vzx
Deposition date deposition_date	2012-10-17
Structure title title	Crystal structure of PcrB from bacillus subtilis subap. subtilis str. 168
Keywords keywords	biosynthesis, prenyltransferases, enzyme catalysis, Transferase; TRANSFERASE
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.

3vzx__assembly_1__model_1

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

Download this curve (.dat)

3vzx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vzx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.18 Å
Rg (electron density)	24.22 Å
Total Rg	25.10 Å
Atom count	3523
Residues	455
Excluded volume	63256 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vzx__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Heptaprenylglyceryl phosphate synthase
Molecular weight formula_weight	25110.6 kDa
EC 编号 ec_number	2.5.1.-
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	4051

MYDVTEWKHVFKLDPNKDLPDEQLEILCESGTDAVIIGGSDGVTEDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKAAALTEADADLNMDDIVAYARVSELLQLPIFYLEYSGVLGDIEAVKKTKAVLETSTLFYGGGIKDAETAKQYAEHADVIVVGNAVYEDFDRALKTVAAVKGE

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	528

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3vzxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d3vzxb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

CATH v4.4 (2 domains)

Domain ID domain_id	3vzxA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	390 — FMN-linked oxidoreductases

Domain ID domain_id	3vzxB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	390 — FMN-linked oxidoreductases

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Unit-cell length a length_a	54.116 Å
Unit-cell length b length_b	55.953 Å
Unit-cell length c length_c	77.271 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.46 °
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	1.540 Å
Low-resolution limit resolution_low	24.570 Å
R factor r_factor	—
R_work r_work	0.1820
R_free r_free	0.2250

Crystal structure of PcrB from bacillus subtilis subap. subtilis str. 168

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

Heptaprenylglyceryl phosphate synthase

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

3vzx__assembly_1__model_1

3vzx__assembly_1__model_1 | I(q)

3vzx__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 PcrB from bacillus subtilis subap. subtilis str. 168

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

Heptaprenylglyceryl phosphate synthase

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

3vzx__assembly_1__model_1

3vzx__assembly_1__model_1 | I(q)

3vzx__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)