2o8r

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

Method: X-RAY DIFFRACTION

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

Polyphosphate kinase

Porphyromonas gingivalis

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 × 13 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MTR1_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–697； UniProt 1–695 Author chain B； PDBConstruct 3–697； UniProt 1–695

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	2o8r
Deposition date deposition_date	2006-12-12
Structure title title	Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis
Keywords keywords	;KINASE, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, NYSGRC, NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM, New York SGX Research Center for Structural Genomics, NYSGXRC, TRANSFERASE ;; TRANSFERASE
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.

2o8r__assembly_1__model_1

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

Download this curve (.dat)

2o8r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o8r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.64 Å
Rg (electron density)	34.63 Å
Total Rg	35.19 Å
Atom count	10350
Residues	1218
Excluded volume	185210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o8r__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	Polyphosphate kinase
Molecular weight formula_weight	82967.0 kDa
EC 编号 ec_number	2.7.4.1
Mutation mutation	M1L, A635T, A690T
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	10452

MSLDVSAYPFFRRDMSWLSFNERVLMEAADRTLPVYDRIKFLSIFSSNLEEFYTVRVAYHQAVLQKRRDRSEAEEDSDADAHILQAIRETVIRQDELYYRIFYDQILPTLEEHGIRLRTHAPTHPDHKAYLRRFFHEEIFPLLYPMLLLPSKVRTFIRSGRVYLAVRLKEKETDEAYSYALLNVPTDGLPRFVELPRLQTDTFYYYSFLEDIIKEHLDVVFPGYEVMDSYSIKVSRDADLLLDAQRPEDLPGEIRKKVKTRKLGAPTRFMYDGRMPDEVLRYICSSCDIDPEEAIRSGNYVNLQDLAMLPNPFAPRLETLTPEPLLSKHLEQAPSLMEGIRRKDYLIHVPYYTYDYVVRLLMEAAISPDVSEIRLTQYRVAENSSIISALEAAAQSGKKVSVFVELKARFDEENNLRLSERMRRSGIRIVYSMPGLKVHAKTALILYHTPAGERPQGIALLSTGNFNETTARIYSDTTLMTANTDIVHDVYRLFRILDGDPEPARFSRLLVARYNMGEAITNLIEREIENVKRGKRGYMLLKMNGLQDKNVITQLYRASEAGVEIDLIVRGICCLVPDMPQSRNIRVTRLVDMYLEHSRIWCFHNGGKEEVFISSADWMKRNLYNRIETACPVLDPTLRREIIDILEIQLRDNIKACRIDSSLNNIYKHNSDEKPVRAQAAIYRYLKGKEETTPAAKEGHHHHHH

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	837
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	13

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2o8ra1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.15 — PPK N-terminal domain-like
Family Family family	a.7.15.1 — PPK N-terminal domain-like

Domain ID domain_id	d2o8ra2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.322 — PHP14-like
Superfamily Superfamily superfamily	d.322.1 — PHP14-like
Family Family family	d.322.1.2 — PPK middle domain-like

Domain ID domain_id	d2o8ra3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

Domain ID domain_id	d2o8ra4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

Domain ID domain_id	d2o8rb1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.15 — PPK N-terminal domain-like
Family Family family	a.7.15.1 — PPK N-terminal domain-like

Domain ID domain_id	d2o8rb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.322 — PHP14-like
Superfamily Superfamily superfamily	d.322.1 — PHP14-like
Family Family family	d.322.1.2 — PPK middle domain-like

Domain ID domain_id	d2o8rb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

Domain ID domain_id	d2o8rb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	2o8rA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	2o8rA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	2o8rB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	310 — Polyphosphate kinase N-terminal domain

Domain ID domain_id	2o8rB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1840 — polyphosphate kinase like
Homologous superfamily homologous superfamily	10 — Polyphosphate kinase middle domain

Domain ID domain_id	2o8rB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	2o8rB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

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Unit-cell length a length_a	99.330 Å
Unit-cell length b length_b	99.330 Å
Unit-cell length c length_c	335.061 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1900
R_work r_work	0.1879
R_free r_free	0.2546

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

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

Polyphosphate kinase

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

2o8r__assembly_1__model_1

2o8r__assembly_1__model_1 | I(q)

2o8r__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 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

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

Polyphosphate kinase

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

2o8r__assembly_1__model_1

2o8r__assembly_1__model_1 | I(q)

2o8r__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 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)