3f4n

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Method: X-RAY DIFFRACTION

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

;Pyridoxine 5'-phosphate synthase ;

Yersinia pestis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXINE-5'-PHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXINE-5'-PHOSPHATE × 2 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXINE-5'-PHOSPHATE × 2 SULFATE ION × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXINE-5'-PHOSPHATE × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 8	PYRIDOXINE-5'-PHOSPHATE × 8 SULFATE ION × 3 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDXJ_YERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–246； UniProt 1–243 Author chain B； PDBConstruct 4–246； UniProt 1–243 Author chain C； PDBConstruct 4–246； UniProt 1–243 Author chain D； PDBConstruct 4–246； UniProt 1–243 Author chain E； PDBConstruct 4–246； UniProt 1–243 Author chain F； PDBConstruct 4–246； UniProt 1–243 Author chain G； PDBConstruct 4–246； UniProt 1–243 Author chain H； PDBConstruct 4–246； UniProt 1–243

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	3f4n
Deposition date deposition_date	2008-11-01
Structure title title	Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis
Keywords keywords	;TIM barrel, Octamer, Pyridoxine biosynthesis, Transferase, CSGID, BIOSYNTHETIC PROTEIN, Structural Genomics, Structural Genomics of National Institute of Allergy and Infectious Diseases, Center for Structural Genomics of Infectious Diseases, NPPSFA, National Project on Protein Structural and Functional Analyses ;; BIOSYNTHETIC PROTEIN, 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.

3f4n__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3f4n__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3f4n__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	25.68 Å
Rg (electron density)	25.21 Å
Total Rg	25.99 Å
Atom count	3689
Residues	483
Excluded volume	65609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3f4n__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3f4n__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3f4n__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3f4n__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3f4n__assembly_5__model_1`	octameric （8）	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	;Pyridoxine 5'-phosphate synthase ;
Molecular weight formula_weight	26602.6 kDa
EC 编号 ec_number	2.6.99.2
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	15591

SNAMADLLLGVNIDHIATLRNARGTIYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTIQTRMNLEMAVTDEMVDIACDIKPHFCCLVPEKRQEVTTEGGLDVAGQVDKMTLAVGRLADVGILVSLFIDADFRQIDAAVAAGAPYIEIHTGAYADASTVLERQAELMRIAKAATYAAGKGLKVNAGHGLTYHNVQPIAALPEMHELNIGHAIIGQAVMTGLAAAVTDMKVLMREARR

Source Source

Source organism organism	Yersinia pestis
NCBI taxonomy ID ncbi_taxonomy_id	632
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXINE-5'-PHOSPHATE
Molecular weight formula_weight	249.2 kDa
Source method src_method	syn
Copy count entity_count	8

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	667

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d3f4na_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4nb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4nc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4nc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3f4nd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4ne_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4nf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4ng_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

Domain ID domain_id	d3f4nh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.24 — Pyridoxine 5'-phosphate synthase
Family Family family	c.1.24.1 — Pyridoxine 5'-phosphate synthase

CATH v4.4 (8 domains)

Domain ID domain_id	3f4nA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nE00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nF00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nG00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3f4nH00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	113.627 Å
Unit-cell length b length_b	114.818 Å
Unit-cell length c length_c	154.316 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.402 Å
Low-resolution limit resolution_low	34.810 Å
R factor r_factor	0.1950
R_work r_work	0.1910
R_free r_free	0.2660

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

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

;Pyridoxine 5'-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

3f4n__assembly_4__model_1

3f4n__assembly_4__model_1 | I(q)

3f4n__assembly_4__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) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

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

;Pyridoxine 5'-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

3f4n__assembly_4__model_1

3f4n__assembly_4__model_1 | I(q)

3f4n__assembly_4__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) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)