1rxo

ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM

Method: X-RAY DIFFRACTION D_max: 132.5 Å Quality: REASONABLE

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

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE

OrganismNot specified

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 B； UniProt 1–475 Chain E； UniProt 1–475 Chain H； UniProt 1–475 Chain L； UniProt 1–475	Non-standard monomer：Yes (specific site not provided by mmCIF)	RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE × 8 （P00870） RUB RIBULOSE-1,5-DIPHOSPHATE × 8 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；14% PEG4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 10 MM CACL2; SOAKED WITH 20 MM RUBP FOR 5 DAYS	Resolution 2.20 Å R-free 0.229

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 1RXO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AA1 ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE Deposited 1997-01-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain L 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 3PG 3-PHOSPHOGLYCERIC ACID × 16	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；14% PEG 4000, 0.2 M NACL, 25 MM HEPES PH 7.8 10 MM MGCL2, 100 MM 3-PHOSPHOGLYCERATE, pH 7.2	Resolution 2.20 Å R-free 0.224
1AUS ACTIVATED UNLIGANDED SPINACH RUBISCO Deposited 1995-06-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain L 1–475（475 aa） Chain M 1–475（475 aa） Chain N 1–475（475 aa） Chain O 1–475（475 aa）	Not recorded	MG MAGNESIUM ION × 8 FMT FORMIC ACID × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.239
1IR1 Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate Deposited 2001-08-31	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）	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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.9；293 K；PEG4000, MgCl2, NaHCO3, DTT, 2-carboxyarabinitol-1,5-bisphosphate, Bicine, pH 7.9, VAPOR DIFFUSION, temperature 293K	Resolution 1.80 Å R-free 0.179
1RBO SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Deposited 1996-10-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain L 1–475（475 aa）	Not recorded	CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；1.7 M (NH4)2SO4, 50 MM PHOSPHATE, PH 7.4 3 MM MGCL2, 25 MM NAHCO3, 10 MM 4CABP	Resolution 2.30 Å R-free 0.171
1RCO SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE Deposited 1996-10-31	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 B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain K 1–475（475 aa） Chain L 1–475（475 aa） Chain O 1–475（475 aa） Chain R 1–475（475 aa） Chain V 1–475（475 aa）	Not recorded	XDP D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；15% PEG 4000, 25 MM HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 20 MM XUBP	Resolution 2.30 Å R-free 0.246
1RCX NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE Deposited 1996-12-06	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 B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain K 1–475（475 aa） Chain L 1–475（475 aa） Chain O 1–475（475 aa） Chain R 1–475（475 aa） Chain V 1–475（475 aa）	Not recorded	RUB RIBULOSE-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；12% PEG 4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 20 MM RUBP	Resolution 2.40 Å R-free 0.237
1UPM ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+. Deposited 2003-10-08	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 B 1–475（475 aa） Chain E 1–475（475 aa） Chain H 1–475（475 aa） Chain K 1–475（475 aa） Chain L 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)	CA CALCIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；10% PEG 4000, 0.1 M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 1MM 2-CABP	Resolution 2.30 Å R-free 0.200
1UPP SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium. Deposited 2003-10-09	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)	CA CALCIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；10% PEG 4000, 0.1M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 0.1 M 3PGA THEN SOAKED IN 2-CABP	Resolution 2.30 Å R-free 0.307
8QJ0 Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO Deposited 2023-09-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain L 1–475（475 aa） Chain M 1–475（475 aa） Chain N 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)	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；SpRub solution at a concentration of 15 mg/mL (in a buffer of 20 mM HEPES, 5 mM MgCl2, pH 8.0), combined reservoir solution (0.2 M MgCl2x6H2O, 0.1 M Tris pH 7.0, 12% w/v PEG 8000	Resolution 2.30 Å R-free 0.227
8RUC ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE Deposited 1996-02-22	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	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.60 Å
9CQ5 Mn-bound RuBisCO from spinach with CABP inhibitor Deposited 2024-07-19	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 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)	MN MANGANESE (II) ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；298 K；PEG 3350, lithium acetate, potassium phosphate	Resolution 2.50 Å R-free 0.242

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBL_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–475； UniProt 1–475 Author chain E； PDBConstruct 1–475； UniProt 1–475 Author chain H； PDBConstruct 1–475； UniProt 1–475 Author chain L； PDBConstruct 1–475； UniProt 1–475

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE

OrganismNot specified

UniProt P00870

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 C； UniProt 58–180 Chain F； UniProt 58–180 Chain I； UniProt 58–180 Chain S； UniProt 58–180	Not recorded	RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE × 8 （P00875） RUB RIBULOSE-1,5-DIPHOSPHATE × 8 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.8；14% PEG4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 10 MM CACL2; SOAKED WITH 20 MM RUBP FOR 5 DAYS	Resolution 2.20 Å R-free 0.229

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1RXO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RBO SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Deposited 1996-10-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C 58–180（123 aa） Chain F 58–180（123 aa） Chain I 58–180（123 aa） Chain S 58–180（123 aa）	Not recorded	CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；1.7 M (NH4)2SO4, 50 MM PHOSPHATE, PH 7.4 3 MM MGCL2, 25 MM NAHCO3, 10 MM 4CABP	Resolution 2.30 Å R-free 0.171
1RCO SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE Deposited 1996-10-31	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 C 58–180（123 aa） Chain F 58–180（123 aa） Chain I 58–180（123 aa） Chain M 58–180（123 aa） Chain P 58–180（123 aa） Chain S 58–180（123 aa） Chain T 58–180（123 aa） Chain W 58–180（123 aa）	Not recorded	XDP D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；15% PEG 4000, 25 MM HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 20 MM XUBP	Resolution 2.30 Å R-free 0.246
1RCX NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE Deposited 1996-12-06	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 C 58–180（123 aa） Chain F 58–180（123 aa） Chain I 58–180（123 aa） Chain M 58–180（123 aa） Chain P 58–180（123 aa） Chain S 58–180（123 aa） Chain T 58–180（123 aa） Chain W 58–180（123 aa）	Not recorded	RUB RIBULOSE-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；12% PEG 4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 20 MM RUBP	Resolution 2.40 Å R-free 0.237
8RUC ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE Deposited 1996-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I 58–180（123 aa） Chain J 58–180（123 aa） Chain K 58–180（123 aa） Chain L 58–180（123 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.60 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBS1_SPIOL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–123； UniProt 58–180 Author chain F； PDBConstruct 1–123； UniProt 58–180 Author chain I； PDBConstruct 1–123； UniProt 58–180 Author chain S； PDBConstruct 1–123； UniProt 58–180

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	1rxo
Deposition date deposition_date	1996-12-06
Structure title title	ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM
Keywords keywords	LYASE (CARBON-CARBON); LYASE (CARBON-CARBON)
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	43.14 Å
Radius of gyration Rg (electron density) rg_electron	42.73 Å
Forward intensity I(0) i0	1004190000.00
Molecular weight molecular_weight	261400.0 kDa
Excluded volume excluded_volume	326270 Å³
Envelope volume envelope_volume	422590 Å³
Hydration-shell volume shell_volume	78011 Å³
Envelope diameter envelope_diameter	137.0 Å
Shell Rg shell_rg	50.95 Å
Envelope Rg envelope_rg	42.83 Å
Shape Rg shape_rg	42.74 Å
Total Rg total_rg	43.05 Å
Total atoms total_atoms	18416
Residues n_residues	2308
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	132.5 Å
Rg (real space) rg_real	42.92 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.0040e+09
I(0) uncertainty (real space) i0_real_error	1.7250e+07
Rg (reciprocal space) rg_reciprocal	43.14 Å
I(0) (reciprocal space) i0_reciprocal	1004000000.0000
Solution quality estimate total_estimate	0.6626
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	60.9 Å
Skewness Skewness skewness	0.097
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	268700000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 0.016; Positv: 1.000; Valcen: 0.983; Smooth: 0.752

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
Molecular weight formula_weight	52777.7 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,B,E,H
Atom count atom_count	19440

MSPQTETKASVGFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAESSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSRGIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV

Entity 2 Entity 2 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
Molecular weight formula_weight	14638.7 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,C,F,I

MQVWPILNLKKYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNREVQCISFIAYKPAGY

Entity 3 Entity 3 non-polymer

Description description	RIBULOSE-1,5-DIPHOSPHATE
Molecular weight formula_weight	310.1 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1024

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1rxob1
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	d1rxob2
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	d1rxoc_
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	d1rxoe1
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	d1rxoe2
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	d1rxof_
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	d1rxoh1
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	d1rxoh2
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	d1rxoi_
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	d1rxol1
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	d1rxol2
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	d1rxos_
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 (12 domains)

Domain ID domain_id	1rxoB01
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	1rxoB02
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	1rxoC00
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	1rxoE01
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	1rxoE02
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	1rxoF00
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	1rxoH01
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	1rxoH02
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	1rxoI00
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	1rxoL01
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	1rxoL02
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	1rxoS00
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 (2)

▶

Unit-cell length a length_a	157.600 Å
Unit-cell length b length_b	158.500 Å
Unit-cell length c length_c	202.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2290

fit	/app/data/saxs_computation/rx/1rxo/1rxo.fit
pddf	/app/data/pr_computation/rx/1rxo/1rxo.pr.out
profile	/app/data/saxs_computation/rx/1rxo/1rxo.dat

ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM

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

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE

State in the Current Structure

Other States of the Same Protein in the Database

RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)