SAXSdb — 2qkl

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

SPBC3B9.21 protein

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SPAC19A8.12 protein × 1 （O13828） LEAD (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9P805_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–127； UniProt 1–127

SPAC19A8.12 protein

Schizosaccharomyces pombe

UniProt O13828

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SPBC3B9.21 protein × 1 （Q9P805） LEAD (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O13828_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–95； UniProt 1–95

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	2qkl
Deposition date deposition_date	2007-07-11
Structure title title	The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex
Keywords keywords	protein-protein complex, 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.

2qkl__assembly_1__model_1

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

Download this curve (.dat)

2qkl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qkl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.15 Å
Rg (electron density)	17.95 Å
Total Rg	18.98 Å
Atom count	1770
Residues	211
Excluded volume	31507 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qkl__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 (4)

Entity 1 Entity 1 polymer

Description description	SPBC3B9.21 protein
Molecular weight formula_weight	15002.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1812

MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SPAC19A8.12 protein
Molecular weight formula_weight	11302.8 kDa
EC 编号 ec_number	3.6.1.30
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTR

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	LEAD (II) ION
Molecular weight formula_weight	207.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	42

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2qklb_
Class class	a — All alpha proteins
Fold Fold fold	a.242 — Dcp2 domain-like
Superfamily Superfamily superfamily	a.242.1 — Dcp2 domain-like
Family Family family	a.242.1.1 — Dcp2 box A domain

CATH v4.4 (2 domains)

Domain ID domain_id	2qklA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	2qklB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1050 — Dcp2, box A domain

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Unit-cell length a length_a	42.723 Å
Unit-cell length b length_b	49.665 Å
Unit-cell length c length_c	115.052 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2290
R_work r_work	0.2270
R_free r_free	0.2590

The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex

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

SPBC3B9.21 protein

State in the Current Structure

Other States of the Same Protein in the Database

SPAC19A8.12 protein

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

2qkl__assembly_1__model_1

2qkl__assembly_1__model_1 | I(q)

2qkl__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex

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

SPBC3B9.21 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SPAC19A8.12 protein

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

2qkl__assembly_1__model_1

2qkl__assembly_1__model_1 | I(q)

2qkl__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)