2vdi

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation

Method: X-RAY DIFFRACTION D_max: 134.2 Å Quality: GOOD

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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

CHLAMYDOMONAS REINHARDTII

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–475 Chain B； UniProt 1–475 Chain C； UniProt 1–475 Chain D； UniProt 1–475 Chain E； UniProt 1–475 Chain F； UniProt 1–475 Chain G； UniProt 1–475 Chain H； UniProt 1–475	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1 × 8 （P00873） MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 43	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.65 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2VDI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GK8 Rubisco from Chlamydomonas reinhardtii Deposited 2001-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain C 1–475（475 aa） Chain E 1–475（475 aa） Chain G 1–475（475 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 66	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4000, 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG/ML PROTEIN	Resolution 1.40 Å R-free 0.162
1IR2 Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP) Deposited 2001-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG4000, HEPES-KOH, glycerol, NaHCO3, MgCl2, DTT, 2-carboxyarabinitol-1,5-bisphosphate (2-CABP), EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.84 Å R-free 0.181
1IR2 Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP) Deposited 2001-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain S 1–475（475 aa） Chain T 1–475（475 aa） Chain U 1–475（475 aa） Chain V 1–475（475 aa） Chain W 1–475（475 aa） Chain X 1–475（475 aa） Chain Y 1–475（475 aa） Chain Z 1–475（475 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG4000, HEPES-KOH, glycerol, NaHCO3, MgCl2, DTT, 2-carboxyarabinitol-1,5-bisphosphate (2-CABP), EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.84 Å R-free 0.181
1UW9 L290F-A222T chlamydomonas Rubisco mutant Deposited 2004-02-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain K 1–475（475 aa） Chain O 1–475（475 aa） Chain R 1–475（475 aa） Chain V 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 55	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；0 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.05 Å R-free 0.194
1UWA L290F mutant rubisco from chlamydomonas Deposited 2004-02-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain K 1–475（475 aa） Chain O 1–475（475 aa） Chain R 1–475（475 aa） Chain V 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 59	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.30 Å R-free 0.205
1UZH A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME Deposited 2004-03-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain K 1–475（475 aa） Chain O 1–475（475 aa） Chain R 1–475（475 aa） Chain V 1–475（475 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 50	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.20 Å R-free 0.193
2V63 Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation Deposited 2007-07-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 EDO 1,2-ETHANEDIOL × 46	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.214
2V67 Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit supressor mutation T342I Deposited 2007-07-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 58	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.208
2V68 Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, T342I Deposited 2007-07-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 49	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.30 Å R-free 0.203
2V69 Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E Deposited 2007-07-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.80 Å R-free 0.228
2V6A Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S Deposited 2007-07-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 59	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.50 Å R-free 0.192
2VDH Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S mutation Deposited 2007-10-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–475（475 aa） Chain B 1–475（475 aa） Chain C 1–475（475 aa） Chain D 1–475（475 aa） Chain E 1–475（475 aa） Chain F 1–475（475 aa） Chain G 1–475（475 aa） Chain H 1–475（475 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 57	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.30 Å R-free 0.203
5BS2 Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL C-terminal tail Deposited 2015-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 462–473（12 aa） Fragment：UNP residues 462-473,UNP residues 44-156 Chain B 462–473（12 aa） Fragment：UNP residues 462-473,UNP residues 44-156 Chain R 462–467（6 aa） Fragment：UNP residues 462-467	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Tris-HCl pH 8.5, 25% PEG2000 MME	Resolution 1.97 Å R-free 0.222
7JFO EPYC1(49-72)-bound Rubisco Deposited 2020-07-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–475（475 aa） Chain C 1–475（475 aa） Chain E 1–475（475 aa） Chain G 1–475（475 aa） Chain I 1–475（475 aa） Chain K 1–475（475 aa） Chain M 1–475（475 aa） Chain O 1–475（475 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.8；200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.13 Å
9HVM In-cell Structure of Pyrenoid Rubisco Deposited 2024-12-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain A 7–475（469 aa） Chain C 7–475（469 aa） Chain E 7–475（469 aa） Chain G 7–475（469 aa） Chain I 7–475（469 aa） Chain K 7–475（469 aa） Chain M 7–475（469 aa） Chain O 7–475（469 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.10 Å

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBL_CHLRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain B； PDBConstruct 1–475； UniProt 1–475 Author chain C； PDBConstruct 1–475； UniProt 1–475 Author chain D； PDBConstruct 1–475； UniProt 1–475 Author chain E； PDBConstruct 1–475； UniProt 1–475 Author chain F； PDBConstruct 1–475； UniProt 1–475 Author chain G； PDBConstruct 1–475； UniProt 1–475 Author chain H； PDBConstruct 1–475； UniProt 1–475

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1

CHLAMYDOMONAS REINHARDTII

UniProt P00873

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain I； UniProt 46–185 Chain J； UniProt 46–185 Chain K； UniProt 46–185 Chain L； UniProt 46–185 Chain M； UniProt 46–185 Chain N； UniProt 46–185 Chain O； UniProt 46–185 Chain P； UniProt 46–185	Non-standard monomer：Yes (specific site not provided by mmCIF)	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 （P00877） MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 43	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.65 Å R-free 0.234

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2VDI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GK8 Rubisco from Chlamydomonas reinhardtii Deposited 2001-08-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Chain K 46–185（140 aa） Chain M 46–185（140 aa） Chain O 46–185（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 66	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4000, 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG/ML PROTEIN	Resolution 1.40 Å R-free 0.162
1UW9 L290F-A222T chlamydomonas Rubisco mutant Deposited 2004-02-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C 46–185（140 aa） Chain F 46–185（140 aa） Chain I 46–185（140 aa） Chain J 46–185（140 aa） Chain M 46–185（140 aa） Chain P 46–185（140 aa） Chain T 46–185（140 aa） Chain W 46–185（140 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 55	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；0 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.05 Å R-free 0.194
1UWA L290F mutant rubisco from chlamydomonas Deposited 2004-02-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C 46–185（140 aa） Chain F 46–185（140 aa） Chain I 46–185（140 aa） Chain J 46–185（140 aa） Chain M 46–185（140 aa） Chain P 46–185（140 aa） Chain T 46–185（140 aa） Chain W 46–185（140 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 59	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.30 Å R-free 0.205
1UZD Chlamydomonas,Spinach Chimeric Rubisco Deposited 2004-03-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C 46–90（45 aa） Chain C 116–185（70 aa） Chain F 46–90（45 aa） Chain F 116–185（70 aa） Chain I 46–90（45 aa） Chain I 116–185（70 aa） Chain J 46–90（45 aa） Chain J 116–185（70 aa） Chain M 46–90（45 aa） Chain M 116–185（70 aa） Chain P 46–90（45 aa） Chain P 116–185（70 aa） Chain T 46–90（45 aa） Chain T 116–185（70 aa） Chain W 46–90（45 aa） Chain W 116–185（70 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 54	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.40 Å R-free 0.230
1UZH A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME Deposited 2004-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C 46–91（46 aa） Chain C 117–185（69 aa） Chain F 46–91（46 aa） Chain F 117–185（69 aa） Chain I 46–91（46 aa） Chain I 117–185（69 aa） Chain J 46–91（46 aa） Chain J 117–185（69 aa） Chain M 46–91（46 aa） Chain M 117–185（69 aa） Chain P 46–91（46 aa） Chain P 117–185（69 aa） Chain T 46–91（46 aa） Chain T 117–185（69 aa） Chain W 46–91（46 aa） Chain W 117–185（69 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 50	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN	Resolution 2.20 Å R-free 0.193
2V63 Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation Deposited 2007-07-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Chain J 46–185（140 aa） Chain K 46–185（140 aa） Chain L 46–185（140 aa） Chain M 46–185（140 aa） Chain N 46–185（140 aa） Chain O 46–185（140 aa） Chain P 46–185（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 EDO 1,2-ETHANEDIOL × 46	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å R-free 0.214
2V67 Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit supressor mutation T342I Deposited 2007-07-13	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Fragment：RESIDUES 46-185 Chain J 46–185（140 aa） Fragment：RESIDUES 46-185 Chain K 46–185（140 aa） Fragment：RESIDUES 46-185 Chain L 46–185（140 aa） Fragment：RESIDUES 46-185 Chain M 46–185（140 aa） Fragment：RESIDUES 46-185 Chain N 46–185（140 aa） Fragment：RESIDUES 46-185 Chain O 46–185（140 aa） Fragment：RESIDUES 46-185 Chain P 46–185（140 aa） Fragment：RESIDUES 46-185	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 58	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.208
2V68 Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, T342I Deposited 2007-07-13	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Fragment：RESIDUES 46-185 Chain J 46–185（140 aa） Fragment：RESIDUES 46-185 Chain K 46–185（140 aa） Fragment：RESIDUES 46-185 Chain L 46–185（140 aa） Fragment：RESIDUES 46-185 Chain M 46–185（140 aa） Fragment：RESIDUES 46-185 Chain N 46–185（140 aa） Fragment：RESIDUES 46-185 Chain O 46–185（140 aa） Fragment：RESIDUES 46-185 Chain P 46–185（140 aa） Fragment：RESIDUES 46-185	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 49	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.30 Å R-free 0.203
2V69 Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E Deposited 2007-07-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Chain J 46–185（140 aa） Chain K 46–185（140 aa） Chain L 46–185（140 aa） Chain M 46–185（140 aa） Chain N 46–185（140 aa） Chain O 46–185（140 aa） Chain P 46–185（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.80 Å R-free 0.228
2V6A Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S Deposited 2007-07-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Chain J 46–185（140 aa） Chain K 46–185（140 aa） Chain L 46–185（140 aa） Chain M 46–185（140 aa） Chain N 46–185（140 aa） Chain O 46–185（140 aa） Chain P 46–185（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 59	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.50 Å R-free 0.192
2VDH Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S mutation Deposited 2007-10-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 46–185（140 aa） Chain J 46–185（140 aa） Chain K 46–185（140 aa） Chain L 46–185（140 aa） Chain M 46–185（140 aa） Chain N 46–185（140 aa） Chain O 46–185（140 aa） Chain P 46–185（140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 57	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.30 Å R-free 0.203
9HVM In-cell Structure of Pyrenoid Rubisco Deposited 2024-12-30	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain B 46–177（132 aa） Chain D 46–177（132 aa） Chain F 46–177（132 aa） Chain H 46–177（132 aa） Chain J 46–177（132 aa） Chain L 46–177（132 aa） Chain N 46–177（132 aa） Chain P 46–177（132 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.10 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBS1_CHLRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–140； UniProt 46–185 Author chain J； PDBConstruct 1–140； UniProt 46–185 Author chain K； PDBConstruct 1–140； UniProt 46–185 Author chain L； PDBConstruct 1–140； UniProt 46–185 Author chain M； PDBConstruct 1–140； UniProt 46–185 Author chain N； PDBConstruct 1–140； UniProt 46–185 Author chain O； PDBConstruct 1–140； UniProt 46–185 Author chain P； PDBConstruct 1–140； UniProt 46–185

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vdi
Deposition date deposition_date	2007-10-09
Structure title title	Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation
Keywords keywords	;VICINAL CYSTEINES, CO2/O2 SPECIFICITY, PHOTOSYNTHESIS, TRANSIT PEPTIDE, PHOTORESPIRATION, METAL-BINDING, HYDROXYLATION, OXIDOREDUCTASE, METHYLATION, CHLOROPLAST, CALVIN CYCLE, MONOOXYGENASE, LYASE, RUBISCO, PLASTID, MAGNESIUM, ACETYLATION, CARBON DIOXIDE FIXATION ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	47.06 Å
Radius of gyration Rg (electron density) rg_electron	46.25 Å
Forward intensity I(0) i0	4323310000.00
Molecular weight molecular_weight	548710.0 kDa
Excluded volume excluded_volume	684360 Å³
Envelope volume envelope_volume	814600 Å³
Hydration-shell volume shell_volume	131420 Å³
Envelope diameter envelope_diameter	137.1 Å
Shell Rg shell_rg	60.15 Å
Envelope Rg envelope_rg	46.17 Å
Shape Rg shape_rg	46.25 Å
Total Rg total_rg	46.59 Å
Total atoms total_atoms	38536
Residues n_residues	4796
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	134.2 Å
Rg (real space) rg_real	46.58 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	4.3230e+09
I(0) uncertainty (real space) i0_real_error	6.8150e+07
Rg (reciprocal space) rg_reciprocal	47.05 Å
I(0) (reciprocal space) i0_reciprocal	4326000000.0000
Solution quality estimate total_estimate	0.8669
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.0 Å
Skewness Skewness skewness	-0.028
Kurtosis Kurtosis kurtosis	-0.583
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3524000000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.455

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
Molecular weight formula_weight	52680.8 kDa
EC 编号 ec_number	4.1.1.39
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	40074

MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYESLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSRGIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL

来源 Source

来源生物 organism	CHLAMYDOMONAS REINHARDTII
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
Molecular weight formula_weight	16283.8 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P

MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRFGSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKTARDFQPANKRSV

来源 Source

来源生物 organism	CHLAMYDOMONAS REINHARDTII
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Molecular weight formula_weight	356.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	43

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1538

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7. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d2vdia1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdia2
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	d2vdib1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdib2
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	d2vdic1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdic2
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	d2vdid1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdid2
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	d2vdie1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdie2
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	d2vdif1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdif2
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	d2vdig1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdig2
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	d2vdih1
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.58.9.0 — automated matches

Domain ID domain_id	d2vdih2
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	d2vdii_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdij_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdik_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdil_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdim_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdin_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdio_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d2vdip_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

CATH v4.4 (24 domains)

Domain ID domain_id	2vdiA01
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	2vdiA02
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	2vdiB01
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	2vdiB02
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	2vdiC01
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	2vdiC02
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	2vdiD01
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	2vdiD02
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	2vdiE01
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	2vdiE02
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	2vdiF01
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	2vdiF02
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	2vdiG01
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	2vdiG02
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	2vdiH01
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	2vdiH02
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	2vdiI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiN00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

Domain ID domain_id	2vdiP00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	10 — Ribulose bisphosphate carboxylase, small subunit

▶

8. Citations (1)

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Unit-cell length a length_a	120.831 Å
Unit-cell length b length_b	178.206 Å
Unit-cell length c length_c	122.917 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2060
R_work r_work	0.2050
R_free r_free	0.2340

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation

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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/vd/2vdi/2vdi.fit
pddf	/app/data/pr_computation/vd/2vdi/2vdi.pr.out
profile	/app/data/saxs_computation/vd/2vdi/2vdi.dat