3zxw

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

Method: X-RAY DIFFRACTION D_max: 133.0 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	Non-standard monomer：Yes (specific site not provided by mmCIF)	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN × 8 （Q8DIS7） 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

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 3ZXW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YBV STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS Deposited 2011-03-10	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） Chain I 1–475（475 aa） Chain K 1–475（475 aa） Chain M 1–475（475 aa） Chain O 1–475（475 aa）	Not recorded	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
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

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

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	Not recorded	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 （Q8DIS5） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3ZXW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YBV STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS Deposited 2011-03-10	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） Chain J 1–118（118 aa） Chain L 1–118（118 aa） Chain N 1–118（118 aa） Chain P 1–118（118 aa）	Not recorded	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

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

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	3zxw
Deposition date deposition_date	2011-08-16
Structure title title	STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Keywords keywords	;CO2/O2 SPECIFICITY, CARBON DIOXIDE FIXATION, PHOTOSYNTHESIS, THERMOSTABILITY, PHOTORESPIRATION, MONOOXYGENASE, HYDROXYLATION, LYASE, 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	43.97 Å
Radius of gyration Rg (electron density) rg_electron	43.48 Å
Forward intensity I(0) i0	950546000.00
Molecular weight molecular_weight	253460.0 kDa
Excluded volume excluded_volume	315940 Å³
Envelope volume envelope_volume	424100 Å³
Hydration-shell volume shell_volume	77124 Å³
Envelope diameter envelope_diameter	133.2 Å
Shell Rg shell_rg	52.13 Å
Envelope Rg envelope_rg	43.04 Å
Shape Rg shape_rg	43.52 Å
Total Rg total_rg	43.69 Å
Total atoms total_atoms	17822
Residues n_residues	2224
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	133.0 Å
Rg (real space) rg_real	43.71 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	9.5050e+08
I(0) uncertainty (real space) i0_real_error	1.4620e+07
Rg (reciprocal space) rg_reciprocal	43.97 Å
I(0) (reciprocal space) i0_reciprocal	950800000.0000
Solution quality estimate total_estimate	0.8866
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.8 Å
Skewness Skewness skewness	0.043
Kurtosis Kurtosis kurtosis	-0.575
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	146800000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.703

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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	53134.3 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	18787

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 CHAIN
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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	905

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3zxwa1
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	d3zxwa2
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	d3zxwb_
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	d3zxwc1
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	d3zxwc2
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	d3zxwd_
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	d3zxwe1
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	d3zxwe2
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	d3zxwf_
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	d3zxwg1
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	d3zxwg2
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	d3zxwh_
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	3zxwA01
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	3zxwA02
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	3zxwB00
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	3zxwC01
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	3zxwC02
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	3zxwD00
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	3zxwE01
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	3zxwE02
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	3zxwF00
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	3zxwG01
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	3zxwG02
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	3zxwH00
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

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8. Citations (1)

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Unit-cell length a length_a	111.500 Å
Unit-cell length b length_b	111.500 Å
Unit-cell length c length_c	397.000 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	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.1828
R_work r_work	0.1810
R_free r_free	0.2135

fit	/app/data/saxs_computation/zx/3zxw/3zxw.fit
pddf	/app/data/pr_computation/zx/3zxw/3zxw.pr.out
profile	/app/data/saxs_computation/zx/3zxw/3zxw.dat

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

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

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) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)