1rf4

Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound State

Method: X-RAY DIFFRACTION

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

5-enolpyruvylshikimate-3-phosphate synthase

Streptococcus pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AROA_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–427； UniProt 1–427 Author chain B； PDBConstruct 1–427； UniProt 1–427 Author chain C； PDBConstruct 1–427； UniProt 1–427 Author chain D； PDBConstruct 1–427； UniProt 1–427

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	1rf4
Deposition date deposition_date	2003-11-07
Structure title title	Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound State
Keywords keywords	shikimate pathway, EPSP synthase, S3P, Glyphosate, PEP, S. pneumoniae, 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.

1rf4__assembly_1__model_1

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

Download this curve (.dat)

1rf4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rf4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.01 Å
Rg (electron density)	21.02 Å
Total Rg	21.80 Å
Atom count	3239
Residues	427
Excluded volume	58095 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rf4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rf4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1rf4__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1rf4__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	5-enolpyruvylshikimate-3-phosphate synthase
Molecular weight formula_weight	45878.8 kDa
EC 编号 ec_number	2.5.1.19
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13729

MKLKTNIRHLHGIIRVPGDKSISHRSIIFGSLAEGETKVYDILRGEDVLSTMQVFRDLGVEIEDKDGVITVQGVGMAGLKAPQNALNMGNSGTSIRLISGVLAGADFEVEMFGDDSLSKRPMDRVTLPLKKMGVSISGQTERDLPPLRLKGTKNLRPIHYELPIASAQVKSALMFAALQAKGESVIIEKEYTRNHTEDMLQQFGGHLSVDGKKITVQGPQKLTGQKVVVPGDISSAAFWLVAGLIAPNSRLVLQNVGINETRTGIIDVIRAMGGKLEITEIDPVAKSATLIVESSDLKGTEICGALIPRLIDELPIIALLATQAQGVTVIKDAEELKVKETDRIQVVADALNSMGADITPTADGMIIKGKSALHGARVNTFGDHRIGMMTAIAALLVADGEVELDRAEAINTSYPSFFDDLESLIHG

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
Molecular weight formula_weight	440.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	773

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rf4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d1rf4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d1rf4c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

Domain ID domain_id	d1rf4d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.2 — EPT/RTPC-like
Family Family family	d.68.2.2 — Enolpyruvate transferase, EPT

CATH v4.4 (8 domains)

Domain ID domain_id	1rf4A01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4A02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4B01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4B02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4C01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4C02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4D01
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

Domain ID domain_id	1rf4D02
Class class	3 — Alpha Beta
Architecture architecture	65 — Alpha-beta prism
Topology topology	10 — UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
Homologous superfamily homologous superfamily	10 — Enolpyruvate transferase domain

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Unit-cell length a length_a	82.495 Å
Unit-cell length b length_b	149.705 Å
Unit-cell length c length_c	88.011 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2140
R_work r_work	0.1960
R_free r_free	0.2360

Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound State

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

5-enolpyruvylshikimate-3-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

1rf4__assembly_1__model_1

1rf4__assembly_1__model_1 | I(q)

1rf4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structural Studies of Streptococcus pneumoniae EPSP Synthase, Tetrahedral intermediate Bound State

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

5-enolpyruvylshikimate-3-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

1rf4__assembly_1__model_1

1rf4__assembly_1__model_1 | I(q)

1rf4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)