SAXSdb — 2woe

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

ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE

RHODOSPIRILLUM RUBRUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 L(+)-TARTARIC ACID × 1 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 ;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DRAG_RHORU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–299； UniProt 1–294 Author chain B； PDBConstruct 6–299； UniProt 1–294 Author chain C； PDBConstruct 6–299； UniProt 1–294

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	2woe
Deposition date deposition_date	2009-07-23
Structure title title	Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose
Keywords keywords	HYDROLASE, DIMANGANESE, NITROGEN FIXATION, ADP-RIBOSYLGLYCOHYDROLASE, MONO-ADP-RIBOSYLHYDROLASE; HYDROLASE
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.

2woe__assembly_1__model_1

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

Download this curve (.dat)

2woe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2woe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.49 Å
Rg (electron density)	17.39 Å
Total Rg	18.28 Å
Atom count	2257
Residues	291
Excluded volume	39779 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2woe__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2woe__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2woe__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
Molecular weight formula_weight	32243.8 kDa
EC 编号 ec_number	3.2.2.24
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7541

GPLGSMTGPSVHDRALGAFLGLAVGDALGATVEFMTKGEIAQQYGIHRKMTGGGWLRLKPGQITDDTEMSLALGRSLAAKGTLDVADICEEFALWLKSRPVNVGNTCRRGIRRYMHEGTTTAPYSEGDAGNGAAMRCLPAALATLGHPADLEPWVLAQARITHNHPLSDAACLTLGRMVHHLIGGRGMKACREEANRLVHQHRDFHFEPYKGQSSAYIVDTMQTVLHYYFVTDTFKSCLIQTVNQGGDADTTGALAGMLAGATYGVDDIPSGWLSKLDMKVEREIRRQVDALLALAGLD

Source Source

Source organism organism	RHODOSPIRILLUM RUBRUM
NCBI taxonomy ID ncbi_taxonomy_id	1085
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	;[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE ;
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	758

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2woea_
Class class	a — All alpha proteins
Fold Fold fold	a.209 — ADP-ribosylglycohydrolase
Superfamily Superfamily superfamily	a.209.1 — ADP-ribosylglycohydrolase
Family Family family	a.209.1.0 — automated matches

Domain ID domain_id	d2woeb_
Class class	a — All alpha proteins
Fold Fold fold	a.209 — ADP-ribosylglycohydrolase
Superfamily Superfamily superfamily	a.209.1 — ADP-ribosylglycohydrolase
Family Family family	a.209.1.0 — automated matches

Domain ID domain_id	d2woec_
Class class	a — All alpha proteins
Fold Fold fold	a.209 — ADP-ribosylglycohydrolase
Superfamily Superfamily superfamily	a.209.1 — ADP-ribosylglycohydrolase
Family Family family	a.209.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2woeA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4080 — ADP-ribosylglycohydrolase fold
Homologous superfamily homologous superfamily	10 — ADP-ribosylation/Crystallin J1

Domain ID domain_id	2woeB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4080 — ADP-ribosylglycohydrolase fold
Homologous superfamily homologous superfamily	10 — ADP-ribosylation/Crystallin J1

Domain ID domain_id	2woeC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	4080 — ADP-ribosylglycohydrolase fold
Homologous superfamily homologous superfamily	10 — ADP-ribosylation/Crystallin J1

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Unit-cell length a length_a	82.110 Å
Unit-cell length b length_b	84.360 Å
Unit-cell length c length_c	146.100 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1691
R_work r_work	0.1671
R_free r_free	0.2073

Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose

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

ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE

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

2woe__assembly_1__model_1

2woe__assembly_1__model_1 | I(q)

2woe__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose

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

ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE

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

2woe__assembly_1__model_1

2woe__assembly_1__model_1 | I(q)

2woe__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)