SAXSdb — 2fdh

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

Alkylated DNA repair protein alkB

Escherichia coli K12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(PTP(MA7)P*T)-3' × 1 MANGANESE (II) ION × 1 2-OXOGLUTARIC ACID × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALKB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–206； UniProt 12–216

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	2fdh
Deposition date deposition_date	2005-12-14
Structure title title	Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
Keywords keywords	;beta jellyroll, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, OXIDOREDUCTASE-DNA COMPLEX ;; OXIDOREDUCTASE/DNA
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.

2fdh__assembly_1__model_1

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

Download this curve (.dat)

2fdh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fdh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.80 Å
Rg (electron density)	15.71 Å
Total Rg	16.80 Å
Atom count	1630
Residues	202
Excluded volume	28735 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fdh__assembly_1__model_1`	dimeric （2）	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	5'-D(PTP(MA7)P*T)-3'
Molecular weight formula_weight	891.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	1855

TAT

Entity 2 Entity 2 polymer

Description description	Alkylated DNA repair protein alkB
Molecular weight formula_weight	23611.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKENLYFQ

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2fdha_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.10 — AlkB-like

CATH v4.4 (1 domains)

Domain ID domain_id	2fdhA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	590 — Alpha-ketoglutarate-dependent dioxygenase AlkB-like

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Unit-cell length a length_a	40.680 Å
Unit-cell length b length_b	40.680 Å
Unit-cell length c length_c	118.300 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	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.240 Å
R factor r_factor	—
R_work r_work	0.1870
R_free r_free	0.2280

Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T

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

Alkylated DNA repair protein alkB

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

2fdh__assembly_1__model_1

2fdh__assembly_1__model_1 | I(q)

2fdh__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T

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

Alkylated DNA repair protein alkB

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

2fdh__assembly_1__model_1

2fdh__assembly_1__model_1 | I(q)

2fdh__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)