1geh

CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)

Method: X-RAY DIFFRACTION

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

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE

Thermococcus kodakarensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	SULFATE ION × 20	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBL_PYRKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–444； UniProt 1–444 Author chain B； PDBConstruct 1–444； UniProt 1–444 Author chain C； PDBConstruct 1–444； UniProt 1–444 Author chain D； PDBConstruct 1–444； UniProt 1–444 Author chain E； PDBConstruct 1–444； UniProt 1–444

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	1geh
Deposition date deposition_date	2000-11-13
Structure title title	CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)
Keywords keywords	Pentagonal toroid decamer, RUBISCO, LYASE; LYASE
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.

1geh__assembly_1__model_1

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

Download this curve (.dat)

1geh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1geh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.78 Å
Rg (electron density)	54.90 Å
Total Rg	55.08 Å
Atom count	33880
Residues	4270
Excluded volume	602280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1geh__assembly_1__model_1`	decameric （10）	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)

Entity 1 Entity 1 polymer

Description description	RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE
Molecular weight formula_weight	49776.5 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	16940

MVEKFDTIYDYYVDKGYEPSKKRDIIAVFRVTPAEGYTIEQAAGAVAAESSTGTWTTLYPWYEQERWADLSAKAYDFHDMGDGSWIVRIAYPFHAFEEANLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIKDRPIYGVVPKPKVGYSPEEFEKLAYDLLSNGADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITADLLEMEQRLEVLADLGLKHAMVDVVITGWGALRYIRDLAADYGLAIHGHRAMHAAFTRNPYHGISMFVLAKLYRLIGIDQLHVGTAGAGKLEGGKWDVIQNARILRESHYKPDENDVFHLEQKFYSIKAAFPTSSGGLHPGNIQPVIEALGTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKWGHVTPV

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

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	10

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1geha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d1geha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d1gehb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d1gehb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d1gehc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d1gehc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d1gehd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d1gehd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d1gehe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d1gehe2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

CATH v4.4 (10 domains)

Domain ID domain_id	1gehA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	1gehA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

Domain ID domain_id	1gehB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	1gehB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

Domain ID domain_id	1gehC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	1gehC02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

Domain ID domain_id	1gehD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	1gehD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

Domain ID domain_id	1gehE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	150 — RuBisCO large subunit, N-terminal domain

Domain ID domain_id	1gehE02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain

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Unit-cell length a length_a	233.750 Å
Unit-cell length b length_b	233.750 Å
Unit-cell length c length_c	93.260 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	30

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.2240
R_free r_free	0.2540

CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)

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

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE

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

1geh__assembly_1__model_1

1geh__assembly_1__model_1 | I(q)

1geh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (2)

CRYSTAL STRUCTURE OF ARCHAEAL RUBISCO (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE)

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

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE

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

1geh__assembly_1__model_1

1geh__assembly_1__model_1 | I(q)

1geh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (2)