2pei

Crystal structure of selenomethionine-labeled RbcX

Method: X-RAY DIFFRACTION

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

ORF134

Synechococcus sp.

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q44177_SYNP2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 1–109 Author chain B； PDBConstruct 1–109； UniProt 1–109 Author chain C； PDBConstruct 1–109； UniProt 1–109 Author chain D； PDBConstruct 1–109； UniProt 1–109 Author chain E； PDBConstruct 1–109； UniProt 1–109 Author chain F； PDBConstruct 1–109； UniProt 1–109 Author chain G； PDBConstruct 1–109； UniProt 1–109 Author chain H； PDBConstruct 1–109； UniProt 1–109 Author chain I； PDBConstruct 1–109； UniProt 1–109 Author chain J； PDBConstruct 1–109； UniProt 1–109 Author chain K； PDBConstruct 1–109； UniProt 1–109 Author chain L； PDBConstruct 1–109； UniProt 1–109

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	2pei
Deposition date deposition_date	2007-04-03
Structure title title	Crystal structure of selenomethionine-labeled RbcX
Keywords keywords	helix bundle, protein complex assembly, chaperone; CHAPERONE
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.

2pei__assembly_1__model_1

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

Download this curve (.dat)

2pei__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pei__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.31 Å
Rg (electron density)	19.45 Å
Total Rg	20.24 Å
Atom count	1673
Residues	208
Excluded volume	30037 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pei__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2pei__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2pei__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2pei__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2pei__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2pei__assembly_6__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 (2)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2peia1
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peib_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peic_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peid_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peie_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peif_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peig_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peih_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peii_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peij_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peik_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

Domain ID domain_id	d2peil_
Class class	a — All alpha proteins
Fold Fold fold	a.280 — RbcX-like
Superfamily Superfamily superfamily	a.280.1 — RbcX-like
Family Family family	a.280.1.1 — RbcX-like

CATH v4.4 (12 domains)

Domain ID domain_id	2peiA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiI00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiJ00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiK00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

Domain ID domain_id	2peiL00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	210 — Chaperonin-like RbcX

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Unit-cell length a length_a	70.362 Å
Unit-cell length b length_b	71.102 Å
Unit-cell length c length_c	113.162 Å
Unit-cell angle α angle_alpha	89.58 °
Unit-cell angle β angle_beta	81.10 °
Unit-cell angle γ angle_gamma	80.09 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2150
R_work r_work	0.2120
R_free r_free	0.2620

Description description	ORF134
Molecular weight formula_weight	12847.2 kDa
Source method src_method	man
Copy count entity_count	12

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	10068

Crystal structure of selenomethionine-labeled RbcX

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

ORF134

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

2pei__assembly_1__model_1

2pei__assembly_1__model_1 | I(q)

2pei__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Synechococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	32049
Host organism host_organism	Escherichia coli BL21(DE3)

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

Crystal structure of selenomethionine-labeled RbcX

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

ORF134

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

2pei__assembly_1__model_1

2pei__assembly_1__model_1 | I(q)

2pei__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)