SAXSdb — 1xaj

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

3-dehydroquinate synthase

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-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	AROB_STAAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–354； UniProt 1–354 Author chain B； PDBConstruct 1–354； UniProt 1–354

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	1xaj
Deposition date deposition_date	2004-08-25
Structure title title	CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE
Keywords keywords	SHIKIMATE PATHWAY, AROMATIC AMINO ACID BIOSYNTHESIS, DHQS, SADHQS, CLOSED FORM, FORM B, DOMAIN MOVEMENT, CYCLASE, LYASE; 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.

1xaj__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1xaj__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xaj__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.85 Å
Rg (electron density)	19.81 Å
Total Rg	20.67 Å
Atom count	2763
Residues	337
Excluded volume	49324 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xaj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xaj__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	3-dehydroquinate synthase
Molecular weight formula_weight	40358.9 kDa
EC 编号 ec_number	4.2.3.4
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	5760

MKLQTTYPSNNYPIYVEHGAIKYIGTYLNQFDQSFLLIDEYVNQYFANKFDDILSYENVHKVIIPAGEKTKTFEQYQETLEYILSHHVTRNTAIIAVGGGATGDFAGFVAATLLRGVHFIQVPTTILAHDSSVGGKVGINSKQGKNLIGAFYRPTAVIYDLDFLKTLPFKQILSGYAEVYKHALLNGESATQDIEQHFKDREILQSLNGMDKYIAKGIETKLDIVVADEKEQGVRKFLNLGHTFGHAVEYYHKIPHGHAVMVGIIYQFIVANALFDSKHDISHYIQYLIQLGYPLDMITDLDFETLYQYMLSDKKNDKQGVQMVLMRQFGDIVVQHVDQLTLQHACEQLKTYFK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
Molecular weight formula_weight	270.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	1xajA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1xajA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
Homologous superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

Domain ID domain_id	1xajB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1xajB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
Homologous superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

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Unit-cell length a length_a	54.738 Å
Unit-cell length b length_b	54.738 Å
Unit-cell length c length_c	231.163 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	25.550 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.3110

CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE

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

3-dehydroquinate 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

1xaj__assembly_2__model_1

1xaj__assembly_2__model_1 | I(q)

1xaj__assembly_2__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF STAPHLYOCOCCUS AUREUS 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD+ AND CARBAPHOSPHONATE

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

3-dehydroquinate 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

1xaj__assembly_2__model_1

1xaj__assembly_2__model_1 | I(q)

1xaj__assembly_2__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)