SAXSdb — 2zkt

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

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 ZINC ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	CALCIUM ION × 3 ZINC ION × 6 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	CALCIUM ION × 3 ZINC ION × 6 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APGM_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–412； UniProt 1–412 Author chain B； PDBConstruct 1–412； UniProt 1–412

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	2zkt
Deposition date deposition_date	2008-03-29
Structure title title	Structure of PH0037 protein from Pyrococcus horikoshii
Keywords keywords	;phosphonopyruvate decarboxylase, ISOMERASE, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; ISOMERASE
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.

2zkt__assembly_3__model_1

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

Download this curve (.dat)

2zkt__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zkt__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	34.09 Å
Rg (electron density)	33.51 Å
Total Rg	34.02 Å
Atom count	8868
Residues	1143
Excluded volume	158720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zkt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zkt__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zkt__assembly_3__model_1`	trimeric （3）	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	2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Molecular weight formula_weight	45488.0 kDa
EC 编号 ec_number	5.4.2.1
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	5720

MVLKRKGLLIILDGLGDRPIKELNGLTPLEYANTPNMDKLAEIGILGQQDPIKPGQPAGSDTAHLSIFGYDPYETYRGRGFFEALGVGLDLSKDDLAFRVNFATLENGIITDRRAGRISTEEAHELARAIQEEVDIGVDFIFKGATGHRAVLVLKGMSRGYKVGDNDPHEAGKPPLKFSYEDEDSKKVAEILEEFVKKAQEVLEKHPINERRRKEGKPIANYLLIRGAGTYPNIPMKFTEQWKVKAAGVIAVALVKGVARAVGFDVYTPEGATGEYNTNEMAKAKKAVELLKDYDFVFLHFKPTDAAGHDNKPKLKAELIERADRMIGYILDHVDLEEVVIAITGDHSTPCEVMNHSGDPVPLLIAGGGVRTDDTKRFGEREAMKGGLGRIRGHDIVPIMMDLMNRSEKFGA

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	221

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2zktA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

Domain ID domain_id	2zktA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2130 — Metalloenzyme domain

Domain ID domain_id	2zktB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	720 — Alkaline Phosphatase, subunit A
Homologous superfamily homologous superfamily	10 — Alkaline Phosphatase, subunit A

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Unit-cell length a length_a	155.900 Å
Unit-cell length b length_b	155.900 Å
Unit-cell length c length_c	230.857 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	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2775
R_work r_work	0.2771
R_free r_free	0.2856

Structure of PH0037 protein from Pyrococcus horikoshii

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

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

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

2zkt__assembly_3__model_1

2zkt__assembly_3__model_1 | I(q)

2zkt__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 (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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure of PH0037 protein from Pyrococcus horikoshii

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

2,3-bisphosphoglycerate-independent phosphoglycerate mutase

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

2zkt__assembly_3__model_1

2zkt__assembly_3__model_1 | I(q)

2zkt__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 (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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)