1u6z

Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation

Method: X-RAY DIFFRACTION

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

Exopolyphosphatase

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	SULFATE ION × 29 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPX_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–513； UniProt 0–512 Author chain B； PDBConstruct 1–513； UniProt 0–512

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	1u6z
Deposition date deposition_date	2004-08-02
Structure title title	Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation
Keywords keywords	;alpha/beta protein, ASKHA (Acetate and Sugar Kinases, Hsc70, Actin) superfamily, HD metal dependent phosphohydrolase superfamily, polyphosphate, twenty-nine sulfates, hydrolase ;; 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.

1u6z__assembly_1__model_1

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

Download this curve (.dat)

1u6z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1u6z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.77 Å
Rg (electron density)	33.23 Å
Total Rg	33.82 Å
Atom count	8084
Residues	998
Excluded volume	143090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1u6z__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 (3)

Entity 1 Entity 1 polymer

Description description	Exopolyphosphatase
Molecular weight formula_weight	58211.9 kDa
EC 编号 ec_number	3.6.1.11
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8984

MPIHDKSPRPQEFAAVDLGSNSFHMVIARVVDGAMQIIGRLKQRVHLADGLGPDNMLSEEAMTRGLNCLSLFAERLQGFSPASVCIVGTHTLRQALNATDFLKRAEKVIPYPIEIISGNEEARLIFMGVEHTQPEKGRKLVIDIGGGSTELVIGENFEPILVESRRMGCVSFAQLYFPGGVINKENFQRARMAAAQKLETLTWQFRIQGWNVAMGASGTIKAAHEVLMEMGEKDGIITPERLEKLVKEVLRHRNFASLSLPGLSEERKTVFVPGLAILCGVFDALAIRELRLSDGALREGVLYEMEGRFRHQDVRSRTASSLANQYHIDSEQARRVLDTTMQMYEQWREQQPKLAHPQLEALLRWAAMLHEVGLNINHSGLHRHSAYILQNSDLPGFNQEQQLMMATLVRYHRKAIKLDDLPRFTLFKKKQFLPLIQLLRLGVLLNNQRQATTTPPTLTLITDDSHWTLRFPHDWFSQNALVLLDLEKEQEYWEGVAGWRLKIEEESTPEIAA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	29

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	634

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1u6za1
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.5 — Ppx associated domain

Domain ID domain_id	d1u6za2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.8 — Ppx/GppA phosphatase

Domain ID domain_id	d1u6za3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.8 — Ppx/GppA phosphatase

Domain ID domain_id	d1u6zb1
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.5 — Ppx associated domain

Domain ID domain_id	d1u6zb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.8 — Ppx/GppA phosphatase

Domain ID domain_id	d1u6zb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.8 — Ppx/GppA phosphatase

CATH v4.4 (8 domains)

Domain ID domain_id	1u6zA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1u6zA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	150 — Exopolyphosphatase. Domain 2

Domain ID domain_id	1u6zA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	1u6zA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2260 —

Domain ID domain_id	1u6zB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	1u6zB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	150 — Exopolyphosphatase. Domain 2

Domain ID domain_id	1u6zB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	1u6zB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2260 —

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Unit-cell length a length_a	89.144 Å
Unit-cell length b length_b	89.144 Å
Unit-cell length c length_c	350.686 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	27.740 Å
R factor r_factor	0.2078
R_work r_work	0.2040
R_free r_free	0.2416

Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation

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

Exopolyphosphatase

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

1u6z__assembly_1__model_1

1u6z__assembly_1__model_1 | I(q)

1u6z__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation

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

Exopolyphosphatase

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

1u6z__assembly_1__model_1

1u6z__assembly_1__model_1 | I(q)

1u6z__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)