1ofr

CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE

Method: X-RAY DIFFRACTION

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

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 PHENYLALANINE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 PHENYLALANINE × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 PHENYLALANINE × 2 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 PHENYLALANINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AROG_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 1–370 Author chain B； PDBConstruct 1–370； UniProt 1–370 Author chain C； PDBConstruct 1–370； UniProt 1–370 Author chain D； PDBConstruct 1–370； UniProt 1–370 Author chain E； PDBConstruct 1–370； UniProt 1–370 Author chain F； PDBConstruct 1–370； UniProt 1–370 Author chain G； PDBConstruct 1–370； UniProt 1–370 Author chain H； PDBConstruct 1–370； UniProt 1–370

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	1ofr
Deposition date deposition_date	2003-04-18
Structure title title	CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE
Keywords keywords	BETA-ALPHA-BARREL, LYASE, AROMATIC AMINO-ACID BIOSYNTHESIS; LYASE
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.

1ofr__assembly_1__model_1

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

Download this curve (.dat)

1ofr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ofr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.04 Å
Rg (electron density)	26.17 Å
Total Rg	27.00 Å
Atom count	5251
Residues	698
Excluded volume	93017 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ofr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ofr__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1ofr__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1ofr__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1ofr__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1ofr__assembly_6__model_1`	tetrameric （4）	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	PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
Molecular weight formula_weight	39797.1 kDa
EC 编号 ec_number	4.1.2.15
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	20930

MSESPMFAANGMPKVNQGAEEDVRILGYDPLASPALLQVQIPATPTSLETAKRGRREAIDIITGKDDRVLVIVGPCSIHDLEAAQEYALRLKKLSDELKGDLSIIMRAYLEKPRTTVGWKGLINDPDVNNTFNINKGLQSARQLFVNLTNIGLPIGSEMLDTISPQYLADLVSFGAIGARTTESQLHRELASGLSFPVGFKNGTDGTLNVAVDACQAAAHSHHFMGVTKHGVAAITTTKGNEHCFVILRGGKKGTNYDAKSVAEAKAQLPAGSNGLMIDYSHGNSNKDFRNQPKVNDVVCEQIANGENAITGVMIESNINEGNQGIPAEGKAGLKYGVSITDACIGWETTEDVLRKLAAAVRQRREVNKK

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	PHENYLALANINE
Molecular weight formula_weight	165.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ofra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofrb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofrc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofrd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofre_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofrf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofrg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

Domain ID domain_id	d1ofrh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.4 — Class I DAHP synthetase

CATH v4.4 (8 domains)

Domain ID domain_id	1ofrA00
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	1ofrB00
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	1ofrC00
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	1ofrD00
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	1ofrE00
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	1ofrF00
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	1ofrG00
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	1ofrH00
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	82.287 Å
Unit-cell length b length_b	94.034 Å
Unit-cell length c length_c	105.121 Å
Unit-cell angle α angle_alpha	65.14 °
Unit-cell angle β angle_beta	85.68 °
Unit-cell angle γ angle_gamma	75.73 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	37.200 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2740

CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE

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

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

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

1ofr__assembly_1__model_1

1ofr__assembly_1__model_1 | I(q)

1ofr__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE

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

PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE

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

1ofr__assembly_1__model_1

1ofr__assembly_1__model_1 | I(q)

1ofr__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)