SAXSdb — 2wvw

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

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

SYNECHOCOCCUS 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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 1–472 Chain B； UniProt 1–472 Chain C； UniProt 1–472 Chain D； UniProt 1–472 Chain E； UniProt 1–472 Chain F； UniProt 1–472 Chain G； UniProt 1–472 Chain H； UniProt 1–472	Not recorded	RBCX PROTEIN × 16 （Q44212）	ELECTRON MICROSCOPY cryo-EM buffer：20 MM TRIS-HCL, PH 8.7；pH 8.7；20 MM TRIS-HCL, PH 8.7 cryo-EM vitrification conditions：Cryogen ETHANE；VITROBOT USED, LIQUID ETHANE	Resolution 9.00 Å

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 2WVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RBL STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301 Deposited 1993-05-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 6–472（467 aa） Chain B 6–472（467 aa） Chain C 6–472（467 aa） Chain D 6–472（467 aa） Chain E 6–472（467 aa） Chain F 6–472（467 aa） Chain G 6–472（467 aa） Chain H 6–472（467 aa）	Not recorded	MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 FMT FORMIC ACID × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1RSC STRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE: THE BINARY COMPLEX BETWEEN ENZYME AND XYLULOSE BISPHOSPHATE Deposited 1994-03-29	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–472（472 aa） Chain B 1–472（472 aa） Chain C 1–472（472 aa） Chain D 1–472（472 aa） Chain E 1–472（472 aa） Chain F 1–472（472 aa） Chain G 1–472（472 aa） Chain H 1–472（472 aa）	Not recorded	XBP XYLULOSE-1,5-BISPHOSPHATE × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
3RG6 Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco Deposited 2011-04-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–472（472 aa） Chain B 1–472（472 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；15-17 % 2-methyl-2,4-pentanediol, 0.1 M KCl, 0.1 M Tris-HCl, pH 8.7, vapor diffusion, temperature 277K	Resolution 3.20 Å R-free 0.245
8ILB The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) Deposited 2023-03-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–472（472 aa） Chain B 1–472（472 aa） Chain C 1–472（472 aa） Chain D 1–472（472 aa） Chain J 1–472（472 aa） Chain K 1–472（472 aa） Chain L 1–472（472 aa） Chain M 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8ILM The cryo-EM structure of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2) Deposited 2023-03-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain A 1–472（472 aa） Chain B 1–472（472 aa） Chain F 1–472（472 aa） Chain G 1–472（472 aa） Chain H 1–472（472 aa） Chain I 1–472（472 aa） Chain J 1–472（472 aa） Chain K 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8IO2 The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL) Deposited 2023-03-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain A 2–472（471 aa） Chain B 2–472（471 aa） Chain C 2–472（471 aa） Chain D 2–472（471 aa） Chain E 2–472（471 aa） Chain F 2–472（471 aa） Chain G 2–472（471 aa） Chain H 2–472（471 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8IOJ The Rubisco assembly intermidiate of Rubisco large subunit (RbcL) and Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) Deposited 2023-03-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–472（472 aa） Chain B 1–472（472 aa） Chain C 1–472（472 aa） Chain D 1–472（472 aa） Chain H 1–472（472 aa） Chain I 1–472（472 aa） Chain J 1–472（472 aa） Chain K 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8IOL The complex of Rubisco large subunit (RbcL) Deposited 2023-03-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–472（472 aa） Chain B 1–472（472 aa） Chain C 1–472（472 aa） Chain D 1–472（472 aa） Chain E 1–472（472 aa） Chain F 1–472（472 aa） Chain G 1–472（472 aa） Chain H 1–472（472 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBL_SYNP6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–472； UniProt 1–472 Author chain B； PDBConstruct 1–472； UniProt 1–472 Author chain C； PDBConstruct 1–472； UniProt 1–472 Author chain D； PDBConstruct 1–472； UniProt 1–472 Author chain E； PDBConstruct 1–472； UniProt 1–472 Author chain F； PDBConstruct 1–472； UniProt 1–472 Author chain G； PDBConstruct 1–472； UniProt 1–472 Author chain H； PDBConstruct 1–472； UniProt 1–472

RBCX PROTEIN

ANABAENA SP. CA

UniProt Q44212

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 × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain I； UniProt 1–135 Chain J； UniProt 1–135 Chain K； UniProt 1–135 Chain L； UniProt 1–135 Chain M； UniProt 1–135 Chain N； UniProt 1–135 Chain O； UniProt 1–135 Chain P； UniProt 1–135 Chain Q； UniProt 1–135 Chain R； UniProt 1–135 Chain S； UniProt 1–135 Chain T； UniProt 1–135 Chain U； UniProt 1–135 Chain V； UniProt 1–135 Chain W； UniProt 1–135 Chain X； UniProt 1–135	Not recorded	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 （P00880）	ELECTRON MICROSCOPY cryo-EM buffer：20 MM TRIS-HCL, PH 8.7；pH 8.7；20 MM TRIS-HCL, PH 8.7 cryo-EM vitrification conditions：Cryogen ETHANE；VITROBOT USED, LIQUID ETHANE	Resolution 9.00 Å

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 2WVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2PEO Crystal structure of RbcX from Anabaena CA Deposited 2007-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；1.0 M Ammonium phosphate, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.298
3HYB Crystal structure of RbcX from Anabaena, crystal form II Deposited 2009-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；1 M (NH4)2SO4, 0.1 M Bis-Tris-HCl pH 5.5, 1 % PEG-3350, vapor diffusion, sitting drop, temperature 291K	Resolution 2.30 Å R-free 0.275
3RG6 Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco Deposited 2011-04-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain C 1–135（135 aa） Chain D 1–135（135 aa） Chain E 1–135（135 aa） Chain F 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；15-17 % 2-methyl-2,4-pentanediol, 0.1 M KCl, 0.1 M Tris-HCl, pH 8.7, vapor diffusion, temperature 277K	Resolution 3.20 Å R-free 0.245

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q44212_9NOST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 21–155； UniProt 1–135 Author chain J； PDBConstruct 21–155； UniProt 1–135 Author chain K； PDBConstruct 21–155； UniProt 1–135 Author chain L； PDBConstruct 21–155； UniProt 1–135 Author chain M； PDBConstruct 21–155； UniProt 1–135 Author chain N； PDBConstruct 21–155； UniProt 1–135 Author chain O； PDBConstruct 21–155； UniProt 1–135 Author chain P； PDBConstruct 21–155； UniProt 1–135 Author chain Q； PDBConstruct 21–155； UniProt 1–135 Author chain R； PDBConstruct 21–155； UniProt 1–135 Author chain S； PDBConstruct 21–155； UniProt 1–135 Author chain T； PDBConstruct 21–155； UniProt 1–135 Author chain U； PDBConstruct 21–155； UniProt 1–135 Author chain V； PDBConstruct 21–155； UniProt 1–135 Author chain W； PDBConstruct 21–155； UniProt 1–135 Author chain X； PDBConstruct 21–155； UniProt 1–135

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2wvw
Deposition date deposition_date	2009-10-20
Structure title title	Cryo-EM structure of the RbcL-RbcX complex
Keywords keywords	;COMPLEX ASSEMBLY, PHOTORESPIRATION, PHOTOSYNTHESIS, DISULFIDE BOND, CARBON FIXATION, LYASE, CHAPERONE, CALVIN CYCLE, CARBON DIOXIDE FIXATION, MONOOXYGENASE, METAL-BINDING, OXIDOREDUCTASE ;; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	57.14 Å
Radius of gyration Rg (electron density) rg_electron	57.05 Å
Forward intensity I(0) i0	4992080000.00
Molecular weight molecular_weight	601520.0 kDa
Excluded volume excluded_volume	754640 Å³
Envelope volume envelope_volume	999300 Å³
Hydration-shell volume shell_volume	138070 Å³
Envelope diameter envelope_diameter	194.4 Å
Shell Rg shell_rg	63.82 Å
Envelope Rg envelope_rg	57.70 Å
Shape Rg shape_rg	57.04 Å
Total Rg total_rg	57.23 Å
Total atoms total_atoms	42392
Residues n_residues	5416
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	191.4 Å
Rg (real space) rg_real	56.95 Å
Rg uncertainty (real space) rg_real_error	1.55 Å
I(0) (real space) i0_real	4.9920e+09
I(0) uncertainty (real space) i0_real_error	1.0020e+08
Rg (reciprocal space) rg_reciprocal	57.28 Å
I(0) (reciprocal space) i0_reciprocal	4995000000.0000
Solution quality estimate total_estimate	0.8649
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	68.4 Å
Skewness Skewness skewness	0.248
Kurtosis Kurtosis kurtosis	-0.306
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	443600000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.782

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
Molecular weight formula_weight	52516.6 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,B,C,D,E,F,G,H
Atom count atom_count	42856

MPKTQSAAGYKAGVKDYKLTYYTPDYTPKDTDLLAAFRFSPQPGVPADEAGAAIAAESSTGTWTTVWTDLLTDMDRYKGKCYHIEPVQGEENSYFAFIAYPLDLFEEGSVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKYGRPMLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKELGMPIIMHDFLTAGFTANTTLAKWCRDNGVLLHIHRAMHAVIDRQRNHGIHFRVLAKCLRLSGGDHLHSGTVVGKLEGDKASTLGFVDLMREDHIEADRSRGVFFTQDWASMPGVLPVASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRDLYREGGDILREAGKWSPELAAALDLWKEIKFEFETMDKL

来源 Source

来源生物 organism	SYNECHOCOCCUS ELONGATUS
NCBI Class编号 ncbi_taxonomy_id	269084
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	RBCX PROTEIN
Molecular weight formula_weight	17694.9 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X

MGSSHHHHHHSSGLVPRGSHMNLKQIAKDTAKTLQSYLTYQALRTVLAQLGETNPPLALWLHNFSAGKVQDGEKYIEELFLEKPDLALRIMTVREHIAEEIAEFLPEMVVTGIQQANMEKRRQHLERMTQVSLSHPSPESEQQQFSDPDWDNLAS

来源 Source

来源生物 organism	ANABAENA SP. CA
NCBI Class编号 ncbi_taxonomy_id	52271
宿主生物 host_organism	ESCHERICHIA COLI

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	9.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	9.00 Å
Resolution测定方法 resolution_method	STANDARD EMAN REFINE PROCEDURE
颗粒数 num_particles	11104

fit	/app/data/saxs_computation/wv/2wvw/2wvw.fit
pddf	/app/data/pr_computation/wv/2wvw/2wvw.pr.out
profile	/app/data/saxs_computation/wv/2wvw/2wvw.dat

Cryo-EM structure of the RbcL-RbcX complex

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

RBCX PROTEIN

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)