SAXSdb — 3o52

▼

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

GDP-mannose pyrophosphatase nudK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	D(-)-TARTARIC ACID × 3 SODIUM ION × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	D(-)-TARTARIC ACID × 2 SODIUM ION × 2 CHLORIDE ION × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	D(-)-TARTARIC ACID × 2 SODIUM ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUDK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 1–191 Author chain B； PDBConstruct 1–191； UniProt 1–191 Author chain C； PDBConstruct 1–191； UniProt 1–191 Author chain D； PDBConstruct 1–191； UniProt 1–191 Author chain E； PDBConstruct 1–191； UniProt 1–191

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3o52
Deposition date deposition_date	2010-07-27
Structure title title	Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate
Keywords keywords	nudix, GDP_mannose, hydrolase, biofilm, tartrate, Nudix fold, GDP-mannose hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3o52__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3o52__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3o52__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	21.82 Å
Rg (electron density)	20.59 Å
Total Rg	21.56 Å
Atom count	2882
Residues	354
Excluded volume	51575 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3o52__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3o52__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3o52__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	GDP-mannose pyrophosphatase nudK
Molecular weight formula_weight	21773.6 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	7421

MTQQITLIKDKILSDNYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYNTKKKTVVLIRQFRVATWVNGNESGQLIESCAGLLDNDEPEVCIRKEAIEETGYEVGEVRKLFELYMSPGGVTELIHFFIAEYSDNQRANAGGGVEDEDIEVLELPFSQALEMIKTGEIRDGKTVLLLNYLQTSHLMD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	D(-)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	197

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3o52a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

Domain ID domain_id	d3o52b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

Domain ID domain_id	d3o52c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

Domain ID domain_id	d3o52d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

Domain ID domain_id	d3o52e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.1 — MutT-like

CATH v4.4 (5 domains)

Domain ID domain_id	3o52A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3o52B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3o52C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3o52D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3o52E00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

▶

Unit-cell length a length_a	75.337 Å
Unit-cell length b length_b	103.218 Å
Unit-cell length c length_c	254.536 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	40

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.730 Å
R factor r_factor	0.2151
R_work r_work	0.2112
R_free r_free	0.2885

Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate

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

GDP-mannose pyrophosphatase nudK

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

3o52__assembly_3__model_1

3o52__assembly_3__model_1 | I(q)

3o52__assembly_3__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate

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

GDP-mannose pyrophosphatase nudK

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

3o52__assembly_3__model_1

3o52__assembly_3__model_1 | I(q)

3o52__assembly_3__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) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)