3shd

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

Method: X-RAY DIFFRACTION

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

Phosphatase nudJ

Escherichia coli

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 × 2 SULFATE ION × 3 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
13	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 SULFATE ION × 6 water × 2	Consistent with protein count
14	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 SULFATE ION × 6 water × 2	Consistent with protein count
15	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 SULFATE ION × 6 water × 2	Consistent with protein count
16	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 SULFATE ION × 6 water × 2	Consistent with protein count
17	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 SULFATE ION × 6 water × 2	Consistent with protein count
18	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 SULFATE ION × 6 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 SULFATE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUDJ_ECOK1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain B； PDBConstruct 1–153； UniProt 1–153 Author chain C； PDBConstruct 1–153； UniProt 1–153 Author chain D； PDBConstruct 1–153； UniProt 1–153 Author chain E； PDBConstruct 1–153； UniProt 1–153 Author chain F； PDBConstruct 1–153； UniProt 1–153 Author chain G； PDBConstruct 1–153； UniProt 1–153 Author chain H； PDBConstruct 1–153； UniProt 1–153 Author chain I； PDBConstruct 1–153； UniProt 1–153 Author chain J； PDBConstruct 1–153； UniProt 1–153 Author chain K； PDBConstruct 1–153； UniProt 1–153 Author chain L； PDBConstruct 1–153； UniProt 1–153

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	3shd
Deposition date deposition_date	2011-06-16
Structure title title	Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
Keywords keywords	Nudix fold, Nudix motif, Hydrolase, (d)NDP/(d)NTP binding, dephosphorylation; 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.

3shd__assembly_10__model_1

Assembly 10 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3shd__assembly_10__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3shd__assembly_10__model_1 | P(r) · Pending

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

Rg（Guinier）	15.99 Å
Rg (electron density)	15.05 Å
Total Rg	16.12 Å
Atom count	1225
Residues	150
Excluded volume	21663 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3shd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3shd__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3shd__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3shd__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3shd__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3shd__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3shd__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3shd__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3shd__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3shd__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3shd__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3shd__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`3shd__assembly_13__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`3shd__assembly_14__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`3shd__assembly_15__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`3shd__assembly_16__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
17	1	`3shd__assembly_17__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
18	1	`3shd__assembly_18__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 (4)

Entity 1 Entity 1 polymer

Description description	Phosphatase nudJ
Molecular weight formula_weight	17450.9 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	14985

MFKPHVTVACVVHAEGKFLVVEETINGKALWNQPAGHLEADETLVEAAARELWEETGISAQPQHFIRMHQWIAPDKTPFLRFLFAIELEQICPTQPHDSDIDCCRWVSAEEILQASNLRSPLVAESIRCYQSGQRYPLEMIGDFNWPFTKGVI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	405955
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	24

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	285

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3shda_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdb_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdc_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdd_
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.113.1.0 — automated matches

Domain ID domain_id	d3shde_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdf_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdg_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdh_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdi_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdj_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdk_
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.113.1.0 — automated matches

Domain ID domain_id	d3shdl_
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.113.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3shdA00
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	3shdB00
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	3shdC00
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	3shdD00
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	3shdE00
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	3shdF00
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	3shdG00
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	3shdH00
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	3shdI00
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	3shdJ00
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	3shdK00
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	3shdL00
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

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Unit-cell length a length_a	111.126 Å
Unit-cell length b length_b	111.126 Å
Unit-cell length c length_c	247.306 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	48

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2297
R_work r_work	0.2264
R_free r_free	0.2915

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

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

Phosphatase nudJ

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

3shd__assembly_10__model_1

3shd__assembly_10__model_1 | I(q)

3shd__assembly_10__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

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

Phosphatase nudJ

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

3shd__assembly_10__model_1

3shd__assembly_10__model_1 | I(q)

3shd__assembly_10__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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)