1SVD: Halothiobacillus neapolitanus RuBisCo

The structure of Halothiobacillus neapolitanus RuBisCo. Determined by X-ray diffraction at 1.8 Å resolution. Released 12 Apr 2005.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Halothiobacillus neapolitanus
Chains: 2
Atoms: 4,778
Mol. weight: 65.85 kDa
Released: 12 Apr 2005

Explore 1SVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SVD contains 30 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	29-37	9	1
α-helix	38	1
α-helix	43-53	11
α-helix	63-67	5
β-strand	76-83	8	1
β-strand	86-96	11	1
α-helix	98-100	3
α-helix	106-114	9
α-helix	117-119	3
β-strand	123-132	10	1
α-helix	135-138	4
α-helix	148-155	8
β-strand	162-166	5	2
α-helix	175-187	13
β-strand	192-194	3	2
β-strand	202	1	3
β-strand	205	1	3
α-helix	207-225	19
β-strand	230-234	5	2
α-helix	240-253	14
β-strand	257-261	5	2
α-helix	267-280	14
β-strand	283-287	5	2
α-helix	291-295	5
β-strand	301-302	2	1
α-helix	304-314	11
β-strand	318-320	3	2
α-helix	329-331	3
α-helix	333-343	11
β-strand	346-347	2	4
β-strand	350	1	5
α-helix	351-353	3
β-strand	355	1	5
β-strand	359-360	2	4
α-helix	364-366	3
β-strand	368-372	5	2
α-helix	377-379	3
α-helix	380-387	8
β-strand	391-394	4	2
α-helix	397-400	4
α-helix	406-425	20
α-helix	434-442	9
α-helix	446-455	10
α-helix	456-458	3

Chain M: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	24-36	13
β-strand	40-46	7	6
α-helix	48-50	3
α-helix	56	1
β-strand	57-59	3	6
α-helix	69-82	14
β-strand	87-94	8	6
β-strand	99-107	9	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	A	protein	473	Halothiobacillus neapolitanus	O85040 (AlphaFold model)
Ribulose bisphosphate carboxylase small chain	M	protein	110	Halothiobacillus neapolitanus	P45686 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1SVD_1 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (chains A)
MAVKKYSAGVKEYRQTYWMPEYTPLDSDILACFKITPQPGVDREEAAAAVAAESSTGTWT
TVWTDLLTDMDYYKGRAYRIEDVPGDDAAFYAFIAYPIDLFEEGSVVNVFTSLVGNVFGF
KAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKYGRPLLGCTIKPKLGLSAKNYGR
AVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTP
EEMYKRAEFAKEIGAPIIMHDYITGGFTANTGLAKWCQDNGVLLHIHRAMHAVIDRNPNH
GIHFRVLTKILRLSGGDHLHTGTVVGKLEGDRASTLGWIDLLRESFIPEDRSRGIFFDQD
WGSMPGVFAVASGGIHVWHMPALVNIFGDDSVLQFGGGTLGHPWGNAAGAAANRVALEAC
VEARNQGRDIEKEGKEILTAAAQHSPELKIAMETWKEIKFEFDTVDKLDTQNR

Sequence of entity 2 (M), FASTA

>1SVD_2 Ribulose bisphosphate carboxylase small chain (chains M)
MAEMQDYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEVKNSMNQYWYMWK
LPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRGN

Primary citation

The structure of Halothiobacillus neapolitanus RuBisCo. Kerfeld, C.A., Sawaya, M.R., Pashkov, I. et al. To be published.

Other PDB entries of the same protein (UniProt O85040 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SMK 1.98 Å, H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex
7SNV 2.07 Å, H. neapolitanus carboxysomal rubisco/CsoSCA-peptide (1-50)complex
6UEW 2.4 Å, Rubisco / CsoS2 N-peptide complex responsible for alpha-carboxysome cargo loading
7ZBT 3.3 Å, Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes

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