3axm

Structure of rice Rubisco in complex with 6PG

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribulose bisphosphate carboxylase large chain

OrganismNot specified

UniProt P0C512

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 16 Ribulose bisphosphate carboxylase small chain, chloroplastic × 8 (Q0INY7) MAGNESIUM ION × 8 6-PHOSPHOGLUCONIC ACID × 8 water × 16 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RBL_ORYSJ
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–477; UniProt 1–477 Author chain B; PDBConstruct 1–477; UniProt 1–477 Author chain C; PDBConstruct 1–477; UniProt 1–477 Author chain D; PDBConstruct 1–477; UniProt 1–477 Author chain E; PDBConstruct 1–477; UniProt 1–477 Author chain F; PDBConstruct 1–477; UniProt 1–477 Author chain G; PDBConstruct 1–477; UniProt 1–477 Author chain H; PDBConstruct 1–477; UniProt 1–477

Ribulose bisphosphate carboxylase small chain, chloroplastic

OrganismNot specified

UniProt Q0INY7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 16 Ribulose bisphosphate carboxylase large chain × 8 (P0C512) MAGNESIUM ION × 8 6-PHOSPHOGLUCONIC ACID × 8 water × 16 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RBS1_ORYSJ
Isoform —
PDB entities 2
Chains and sequence ranges Author chain S; PDBConstruct 2–129; UniProt 48–175 Author chain T; PDBConstruct 2–129; UniProt 48–175 Author chain U; PDBConstruct 2–129; UniProt 48–175 Author chain V; PDBConstruct 2–129; UniProt 48–175 Author chain W; PDBConstruct 2–129; UniProt 48–175 Author chain X; PDBConstruct 2–129; UniProt 48–175 Author chain Y; PDBConstruct 2–129; UniProt 48–175 Author chain Z; PDBConstruct 2–129; UniProt 48–175

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_id3axm
Deposition date deposition_date2011-04-11
Structure title titleStructure of rice Rubisco in complex with 6PG
Keywords keywordsalpha/beta barrel, photosynthetic carbon reduction, Lyase; LYASE
Experimental Method methodX-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.

3axm__assembly_1__model_1

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

Download this curve (.dat)

3axm__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3axm__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)46.41 Å
Rg (electron density)45.85 Å
Total Rg46.24 Å
Atom count35950
Residues4512
Excluded volume639150 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3axm__assembly_1__model_1 hexadecameric (16) 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 (5)

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd3axma1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axma2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axmb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axmb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axmc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axmc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axmd1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axmd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axme1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axme2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axmf1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axmf2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axmg1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axmg2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axmh1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd3axmh2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd3axms_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmt_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmu_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmv_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmw_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmx_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmy_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd3axmz_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit

CATH v4.4 (24 domains)

Domain ID domain_id3axmA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmC02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmD02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmE02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmF02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmG02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id3axmH02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id3axmS00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmT00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmU00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmV00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmW00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmX00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmY00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id3axmZ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
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7. Citations (1)