2ybv

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

Method: X-RAY DIFFRACTION D_max: 134.3 Å Quality: GOOD

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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

THERMOSYNECHOCOCCUS ELONGATUS

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 C； UniProt 1–475 Chain E； UniProt 1–475 Chain G； UniProt 1–475 Chain I； UniProt 1–475 Chain K； UniProt 1–475 Chain M； UniProt 1–475 Chain O； UniProt 1–475	Not recorded	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT × 8 （Q8DIS7） CL CHLORIDE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；5% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7	Resolution 2.30 Å R-free 0.232

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 2YBV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZXW STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Deposited 2011-08-16	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 GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；80 MM HEPES, 20 MM MGCL2, 8% (W/V) PEG4000, 30% (V/V) GLYCEROL, PH=8	Resolution 2.10 Å R-free 0.213
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	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 A1 1–475（475 aa） Fragment：RbcL Chain A2 1–475（475 aa） Fragment：RbcL Chain A3 1–475（475 aa） Fragment：RbcL Chain A4 1–475（475 aa） Fragment：RbcL Chain A5 1–475（475 aa） Fragment：RbcL Chain A6 1–475（475 aa） Fragment：RbcL Chain A7 1–475（475 aa） Fragment：RbcL Chain A8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain S1 1–475（475 aa） Fragment：RbcL Chain S2 1–475（475 aa） Fragment：RbcL Chain S3 1–475（475 aa） Fragment：RbcL Chain S4 1–475（475 aa） Fragment：RbcL Chain S5 1–475（475 aa） Fragment：RbcL Chain S6 1–475（475 aa） Fragment：RbcL Chain S7 1–475（475 aa） Fragment：RbcL Chain S8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain C1 1–475（475 aa） Fragment：RbcL Chain C2 1–475（475 aa） Fragment：RbcL Chain C3 1–475（475 aa） Fragment：RbcL Chain C4 1–475（475 aa） Fragment：RbcL Chain C5 1–475（475 aa） Fragment：RbcL Chain C6 1–475（475 aa） Fragment：RbcL Chain C7 1–475（475 aa） Fragment：RbcL Chain C8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain E1 1–475（475 aa） Fragment：RbcL Chain E2 1–475（475 aa） Fragment：RbcL Chain E3 1–475（475 aa） Fragment：RbcL Chain E4 1–475（475 aa） Fragment：RbcL Chain E5 1–475（475 aa） Fragment：RbcL Chain E6 1–475（475 aa） Fragment：RbcL Chain E7 1–475（475 aa） Fragment：RbcL Chain E8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain G1 1–475（475 aa） Fragment：RbcL Chain G2 1–475（475 aa） Fragment：RbcL Chain G3 1–475（475 aa） Fragment：RbcL Chain G4 1–475（475 aa） Fragment：RbcL Chain G5 1–475（475 aa） Fragment：RbcL Chain G6 1–475（475 aa） Fragment：RbcL Chain G7 1–475（475 aa） Fragment：RbcL Chain G8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain I1 1–475（475 aa） Fragment：RbcL Chain I2 1–475（475 aa） Fragment：RbcL Chain I3 1–475（475 aa） Fragment：RbcL Chain I4 1–475（475 aa） Fragment：RbcL Chain I5 1–475（475 aa） Fragment：RbcL Chain I6 1–475（475 aa） Fragment：RbcL Chain I7 1–475（475 aa） Fragment：RbcL Chain I8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain K1 1–475（475 aa） Fragment：RbcL Chain K2 1–475（475 aa） Fragment：RbcL Chain K3 1–475（475 aa） Fragment：RbcL Chain K4 1–475（475 aa） Fragment：RbcL Chain K5 1–475（475 aa） Fragment：RbcL Chain K6 1–475（475 aa） Fragment：RbcL Chain K7 1–475（475 aa） Fragment：RbcL Chain K8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain M1 1–475（475 aa） Fragment：RbcL Chain M2 1–475（475 aa） Fragment：RbcL Chain M3 1–475（475 aa） Fragment：RbcL Chain M4 1–475（475 aa） Fragment：RbcL Chain M5 1–475（475 aa） Fragment：RbcL Chain M6 1–475（475 aa） Fragment：RbcL Chain M7 1–475（475 aa） Fragment：RbcL Chain M8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain O1 1–475（475 aa） Fragment：RbcL Chain O2 1–475（475 aa） Fragment：RbcL Chain O3 1–475（475 aa） Fragment：RbcL Chain O4 1–475（475 aa） Fragment：RbcL Chain O5 1–475（475 aa） Fragment：RbcL Chain O6 1–475（475 aa） Fragment：RbcL Chain O7 1–475（475 aa） Fragment：RbcL Chain O8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain Q1 1–475（475 aa） Fragment：RbcL Chain Q2 1–475（475 aa） Fragment：RbcL Chain Q3 1–475（475 aa） Fragment：RbcL Chain Q4 1–475（475 aa） Fragment：RbcL Chain Q5 1–475（475 aa） Fragment：RbcL Chain Q6 1–475（475 aa） Fragment：RbcL Chain Q7 1–475（475 aa） Fragment：RbcL Chain Q8 1–475（475 aa） Fragment：RbcL	Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A Mutation：F345I / P415A	ZN ZINC ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0	Resolution 2.63 Å R-free 0.274

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

View Construct and Data Evidence

UniProt name	RBL_THEEB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain C； PDBConstruct 1–475； UniProt 1–475 Author chain E； PDBConstruct 1–475； UniProt 1–475 Author chain G； PDBConstruct 1–475； UniProt 1–475 Author chain I； PDBConstruct 1–475； UniProt 1–475 Author chain K； PDBConstruct 1–475； UniProt 1–475 Author chain M； PDBConstruct 1–475； UniProt 1–475 Author chain O； PDBConstruct 1–475； UniProt 1–475

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT

THERMOSYNECHOCOCCUS ELONGATUS

UniProt Q8DIS7

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 1–118 Chain D； UniProt 1–118 Chain F； UniProt 1–118 Chain H； UniProt 1–118 Chain J； UniProt 1–118 Chain L； UniProt 1–118 Chain N； UniProt 1–118 Chain P； UniProt 1–118	Not recorded	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 （Q8DIS5） CL CHLORIDE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；5% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7	Resolution 2.30 Å R-free 0.232

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2YBV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZXW STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Deposited 2011-08-16	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 1–118（118 aa） Chain D 1–118（118 aa） Chain F 1–118（118 aa） Chain H 1–118（118 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；80 MM HEPES, 20 MM MGCL2, 8% (W/V) PEG4000, 30% (V/V) GLYCEROL, PH=8	Resolution 2.10 Å R-free 0.213

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8DIS7_THEEB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118 Author chain D； PDBConstruct 1–118； UniProt 1–118 Author chain F； PDBConstruct 1–118； UniProt 1–118 Author chain H； PDBConstruct 1–118； UniProt 1–118 Author chain J； PDBConstruct 1–118； UniProt 1–118 Author chain L； PDBConstruct 1–118； UniProt 1–118 Author chain N； PDBConstruct 1–118； UniProt 1–118 Author chain P； PDBConstruct 1–118； UniProt 1–118

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	2ybv
Deposition date deposition_date	2011-03-10
Structure title title	STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS
Keywords keywords	;CO2/O2 SPECIFICITY, CARBON DIOXIDE FIXATION, PHOTOSYNTHESIS, THERMOSTABILITY, PHOTORESPIRATION, MONOOXYGENASE, HYDROXYLATION, OXIDOREDUCTASE, LYASE, RUBISCO, CHLOROPLAST, CALVIN CYCLE, THERMOPHILIC CYANOBACTERIA ;; 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	47.10 Å
Radius of gyration Rg (electron density) rg_electron	46.18 Å
Forward intensity I(0) i0	3313680000.00
Molecular weight molecular_weight	479880.0 kDa
Excluded volume excluded_volume	598630 Å³
Envelope volume envelope_volume	747730 Å³
Hydration-shell volume shell_volume	122720 Å³
Envelope diameter envelope_diameter	137.3 Å
Shell Rg shell_rg	58.90 Å
Envelope Rg envelope_rg	45.63 Å
Shape Rg shape_rg	46.20 Å
Total Rg total_rg	46.47 Å
Total atoms total_atoms	33751
Residues n_residues	4256
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	134.3 Å
Rg (real space) rg_real	46.62 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	3.3140e+09
I(0) uncertainty (real space) i0_real_error	4.4660e+07
Rg (reciprocal space) rg_reciprocal	47.09 Å
I(0) (reciprocal space) i0_reciprocal	3316000000.0000
Solution quality estimate total_estimate	0.8655
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.1 Å
Skewness Skewness skewness	-0.021
Kurtosis Kurtosis kurtosis	-0.557
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	1117000000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.433

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
Molecular weight formula_weight	53091.3 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	A,C,E,G,I,K,M,O
Atom count atom_count	34583

MAYTQSKSQKVGYQAGVKDYRLTYYTPDYTPKDTDILAAFRVTPQPGVPFEEAAAAVAAESSTGTWTTVWTDLLTDLDRYKGCCYDIEPLPGEDNQFIAYIAYPLDLFEEGSVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKELEMPIIMHDFLTAGFTANTTLSKWCRDNGMLLHIHRAMHAVMDRQKNHGIHFRVLAKCLRMSGGDHIHTGTVVGKLEGDKAVTLGFVDLLRENYIEQDRSRGIYFTQDWASMPGVMAVASGGIHVWHMPALVDIFGDDAVLQFGGGTLGHPWGNAPGATANRVALEACIQARNEGRDLMREGGDIIREAARWSPELAAACELWKEIKFEFEAQDTI

来源 Source

来源生物 organism	THERMOSYNECHOCOCCUS ELONGATUS
NCBI Class编号 ncbi_taxonomy_id	197221
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
Molecular weight formula_weight	13999.8 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	B,D,F,H,J,L,N,P

MKTLPKERRYETFSYLPPLSDAQIARQIQYAIDQGYHPCVEFNETSNAEIRYWTMWKLPLFNCTNAQDVLNEVQQCRSEYPNCFIRVVAFDNIKQCQVMSFIVYKPNQANSGYSGYRY

来源 Source

来源生物 organism	THERMOSYNECHOCOCCUS ELONGATUS
NCBI Class编号 ncbi_taxonomy_id	197221
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	832

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7. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d2ybva1
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	d2ybva2
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	d2ybvb_
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	d2ybvc1
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	d2ybvc2
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	d2ybvd_
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	d2ybve1
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	d2ybve2
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	d2ybvf_
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	d2ybvg1
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	d2ybvg2
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	d2ybvh_
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	d2ybvi1
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	d2ybvi2
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	d2ybvj_
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	d2ybvk1
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	d2ybvk2
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	d2ybvl_
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	d2ybvm1
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	d2ybvm2
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	d2ybvn_
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	d2ybvo1
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	d2ybvo2
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	d2ybvp_
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	2ybvA01
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	2ybvA02
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	2ybvB00
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	2ybvC01
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	2ybvC02
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	2ybvD00
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	2ybvE01
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	2ybvE02
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	2ybvF00
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	2ybvG01
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	2ybvG02
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	2ybvH00
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	2ybvI01
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	2ybvI02
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	2ybvJ00
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	2ybvK01
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	2ybvK02
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	2ybvL00
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	2ybvM01
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	2ybvM02
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	2ybvN00
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	2ybvO01
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	2ybvO02
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	2ybvP00
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)

▶

Unit-cell length a length_a	115.480 Å
Unit-cell length b length_b	163.470 Å
Unit-cell length c length_c	163.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.96 °
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	2.300 Å
Low-resolution limit resolution_low	39.840 Å
R factor r_factor	0.1976
R_work r_work	0.1958
R_free r_free	0.2317

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

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 SUBUNIT

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 (4)

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 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/yb/2ybv/2ybv.fit
pddf	/app/data/pr_computation/yb/2ybv/2ybv.pr.out
profile	/app/data/saxs_computation/yb/2ybv/2ybv.dat