SAXSdb — 1wfx

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

;Probable RNA 2'-phosphotransferase ;

Aeropyrum pernix

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 CHLORIDE ION × 5 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	ZINC ION × 3 CHLORIDE ION × 15 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KPTA_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 35–220

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	1wfx
Deposition date deposition_date	2004-05-27
Structure title title	Crystal Structure of APE0204 from Aeropyrum pernix
Keywords keywords	;RNA 2'-phosphotransferase, tRNA splicing, NAD, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

1wfx__assembly_2__model_1

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

Download this curve (.dat)

1wfx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wfx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.04 Å
Rg (electron density)	28.32 Å
Total Rg	29.25 Å
Atom count	4342
Residues	531
Excluded volume	77426 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wfx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wfx__assembly_2__model_1`	trimeric （3）	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	;Probable RNA 2'-phosphotransferase ;
Molecular weight formula_weight	21398.2 kDa
EC 编号 ec_number	2.7.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1464

MRVRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNGEIRARYGHSIPVNVEPLPGEPPPILYHGTTEEALPLIMERGIMRGRRLKVHLTSSLEDAVSTGRRHGNLVAVLLVDVECLRRRGLKVERMSKTVYTVDWVPPECIAEVRRESLGRSL

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	56636
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	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wfxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.5 — Tpt1/KptA

CATH v4.4 (2 domains)

Domain ID domain_id	1wfxA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	970 — RNA 2'-phosphotransferase, Tpt1/KptA family, N-terminal domain

Domain ID domain_id	1wfxA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	170 — ADP-ribosylation fold
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	102.667 Å
Unit-cell length b length_b	102.667 Å
Unit-cell length c length_c	101.489 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	44.070 Å
R factor r_factor	—
R_work r_work	0.2200
R_free r_free	0.2860

Crystal Structure of APE0204 from Aeropyrum pernix

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

;Probable RNA 2'-phosphotransferase ;

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

1wfx__assembly_2__model_1

1wfx__assembly_2__model_1 | I(q)

1wfx__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of APE0204 from Aeropyrum pernix

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

;Probable RNA 2'-phosphotransferase ;

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

1wfx__assembly_2__model_1

1wfx__assembly_2__model_1 | I(q)

1wfx__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)