SAXSdb — 2irp

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

Putative aldolase class 2 protein aq_1979

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 4 BETA-MERCAPTOETHANOL × 4 water × 4	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 BETA-MERCAPTOETHANOL × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	CHLORIDE ION × 8 BETA-MERCAPTOETHANOL × 8 water × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 4 BETA-MERCAPTOETHANOL × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1979_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–208； UniProt 1–208 Author chain B； PDBConstruct 1–208； UniProt 1–208

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	2irp
Deposition date deposition_date	2006-10-16
Structure title title	Crystal structure of the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5
Keywords keywords	;aldolase, aldehyde, enzymatic mechanism, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2irp__assembly_2__model_1

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

Download this curve (.dat)

2irp__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2irp__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.72 Å
Rg (electron density)	16.63 Å
Total Rg	17.82 Å
Atom count	1640
Residues	204
Excluded volume	29525 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2irp__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2irp__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2irp__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2irp__assembly_4__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	Putative aldolase class 2 protein aq_1979
Molecular weight formula_weight	23676.8 kDa
EC 编号 ec_number	4.1.2.17
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	3630

MNVELFKKFSEKVEEIIEAGRILHSRGWVPATSGNISAKVSEEYIAITASGKHKGKLTPEDILLIDYEGRPVGGGKPSAETLLHTTVYKLFPEVNAVVHTHSPNATVISIVEKKDFVELEDYELLKAFPDIHTHEVKIKIPIFPNEQNIPLLAKEVENYFKTSEDKYGFLIRGHGLYTWGRSMEEALIHTEALEFIFECELKLLSFHS

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2irpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.0 — automated matches

Domain ID domain_id	d2irpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.74 — AraD/HMP-PK domain-like
Superfamily Superfamily superfamily	c.74.1 — AraD/HMP-PK domain-like
Family Family family	c.74.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2irpA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

Domain ID domain_id	2irpB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	225 — L-fuculose-1-phosphate Aldolase
Homologous superfamily homologous superfamily	10 — Class II aldolase/adducin N-terminal domain

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Unit-cell length a length_a	102.500 Å
Unit-cell length b length_b	102.500 Å
Unit-cell length c length_c	116.045 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	16

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.340 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2520

Crystal structure of the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5

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

Putative aldolase class 2 protein aq_1979

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

2irp__assembly_2__model_1

2irp__assembly_2__model_1 | I(q)

2irp__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 (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 the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5

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

Putative aldolase class 2 protein aq_1979

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

2irp__assembly_2__model_1

2irp__assembly_2__model_1 | I(q)

2irp__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 (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)