1SVD - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE STRUCTURE OF HALOTHIOBACILLUS NEAPOLITANUS RUBISCO

Authors :   C. A. Kerfeld, M. R. Sawaya, I. Pashkov, G. Cannon, E. Williams, K. Tran, T. O. Yeates

Date :   29 Mar 04 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,M
Biol. Unit 1: A,M  (1x)
Biol. Unit 2: A,M  (8x)
Biol. Unit 3: A,M  (2x)
Biol. Unit 4: A,M  (2x)

Keywords :   Beta-Alpha-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Kerfeld, M. R. Sawaya, I. Pashkov, G. Cannon, E. Williams, K. Tran T. O. Yeates
The Structure Of Halothiobacillus Neapolitanus Rubisco
To Be Published
PubMed: search

Molecule 1 - RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE SUBUNIT
	Chains	:	A
	EC Number	:	4.1.1.39
	Organism Scientific	:	HALOTHIOBACILLUS NEAPOLITANUS
	Organism Taxid	:	927

Molecule 2 - RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
	Chains	:	M
	EC Number	:	4.1.1.39
	Organism Scientific	:	HALOTHIOBACILLUS NEAPOLITANUS
	Organism Taxid	:	927
	Synonym	:	RUBISCO SMALL SUBUNIT

		1	2
Asymmetric Unit	:	A	M
Biological Unit 1 (1x)	:	A	M
Biological Unit 2 (8x)	:	A	M
Biological Unit 3 (2x)	:	A	M
Biological Unit 4 (2x)	:	A	M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 24)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	SO4	16	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:288 , HIS A:320 , SER A:372 , HOH A:555 , HOH A:573 , HOH A:646 , HOH A:725	BINDING SITE FOR RESIDUE SO4 A 474
2	AC2	SOFTWARE	GLY A:374 , GLY A:396 , GLY A:397 , HOH A:527 , HOH A:572	BINDING SITE FOR RESIDUE SO4 A 475
3	AC3	SOFTWARE	ASN A:156 , HOH A:642 , HOH A:704 , TYR M:13 , SER M:51 , LYS M:89 , HOH M:135	BINDING SITE FOR RESIDUE GOL M 111

(no "SS Bond" information available for 1SVD)

Asymmetric Unit

No.	Residues
1	Lys A:168	-	Pro A:169

(no "SAP(SNP)/Variant" information available for 1SVD)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL1_HALNC	189-197	1	A:189-197

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL1_HALNC	189-197	1	A:189-197

Biological Unit 2 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL1_HALNC	189-197	8	A:189-197

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL1_HALNC	189-197	2	A:189-197

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RUBISCO_LARGE	PS00157	Ribulose bisphosphate carboxylase large chain active site.	RBL1_HALNC	189-197	2	A:189-197

(no "Exon" information available for 1SVD)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:445
 aligned with RBL1_HALNC | O85040 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:445
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455     
           RBL1_HALNC    16 TYWMPEYTPLDSDILACFKITPQPGVDREEAAAAVAAESSTGTWTTVWTDLLTDMDYYKGRAYRIEDVPGDDAAFYAFIAYPIDLFEEGSVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEIGAPIIMHDYITGGFTANTGLAKWCQDNGVLLHIHRAMHAVIDRNPNHGIHFRVLTKILRLSGGDHLHTGTVVGKLEGDRASTLGWIDLLRESFIPEDRSRGIFFDQDWGSMPGVFAVASGGIHVWHMPALVNIFGDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVEARNQGRDIEKEGKEILTAAAQHSPELKIAMETWKEIKF 460
               SCOP domains d1svda2 A:16-142 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                               d1svda1 A:143-460 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1svdA01 A:16-140  [code=3.30.70.150, no name defined]                                                                        --1svdA02 A:143-460 Rubisco                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains RuBisCO_large_N-1svdA02 A:16-139                                                                                            -------RuBisCO_large-1svdA01 A:147-455                                                                                                                                                                                                                                                                                      ----- Pfam domains
         Sec.struct. author .............eeeeeeeee....hhhhhhhhhhhhh.......hhhhhhh.......eeeeeeee..eeeeeeeeeeehhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhh....eehhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh.ee..hhhhh....ee.......eeeee...hhhhhhhhhhhhh..eeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------RUBISCO_L----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svd A  16 TYWMPEYTPLDSDILACFKITPQPGVDREEAAAAVAAESSTGTWTTVWTDLLTDMDYYKGRAYRIEDVPGDDAAFYAFIAYPIDLFEEGSVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKYGRPLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEIGAPIIMHDYITGGFTANTGLAKWCQDNGVLLHIHRAMHAVIDRNPNHGIHFRVLTKILRLSGGDHLHTGTVVGKLEGDRASTLGWIDLLRESFIPEDRSRGIFFDQDWGSMPGVFAVASGGIHVWHMPALVNIFGDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVEARNQGRDIEKEGKEILTAAAQHSPELKIAMETWKEIKF 460
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455

Chain M from PDB  Type:PROTEIN  Length:108
 aligned with RBS_HALNC | P45686 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:108
                                    12        22        32        42        52        62        72        82        92       102        
            RBS_HALNC     3 EMQDYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEVKNSMNQYWYMWKLPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRGN 110
               SCOP domains d1svdm1 M:3-110 Ribulose 1,5-bisphosphate carboxylase-oxygenase                                              SCOP domains
               CATH domains 1svdM00 M:3-110  [code=3.30.190.10, no name defined]                                                         CATH domains
               Pfam domains ---------RuBisCO_small-1svdM01 M:12-110                                                                      Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhh..eeeeeeehhhhh.....eee........hhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1svd M   3 EMQDYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIEHVEVKNSMNQYWYMWKLPFFGEQNVDNVLAEIEACRSAYPTHQVKLVAYDNYAQSLGLAFVVYRGN 110
                                    12        22        32        42        52        62        72        82        92       102

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit(hide GO term definitions)

Chain A (RBL1_HALNC | O85040)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016984	ribulose-bisphosphate carboxylase activity	Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
	GO:0015977	carbon fixation	A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019253	reductive pentose-phosphate cycle	The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.

Chain M (RBS_HALNC | P45686)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016984	ribulose-bisphosphate carboxylase activity	Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
	GO:0015977	carbon fixation	A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019253	reductive pentose-phosphate cycle	The fixation of carbon dioxide (CO2) as glucose in the chloroplasts of C3 plants; uses ATP and NADPH formed in the light reactions of photosynthesis; carbon dioxide reacts with ribulose 1,5-bisphosphate (catalyzed by the function of ribulose-bisphosphate carboxylase) to yield two molecules of 3-phosphoglycerate; these are then phosphorylated by ATP to 1,3-bisphosphateglyceraldehyde which, in turn, is then reduced by NADPH to glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate is converted to fructose 5-phosphate and ribulose 5-phosphate by aldolase and other enzymes; the ribulose 5-phosphate is phosphorylated by ATP to ribulose 1,5-bisphosphate.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:168 - Pro A:169	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1svd
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RBL1_HALNC \| O85040
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	RBS_HALNC \| P45686
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.1.1.39
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RBL1_HALNC \| O85040
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RBS_HALNC \| P45686
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1SVD)

(no "Related Entries Specified in the PDB File" available for 1SVD)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (3, 3)

Gene Ontology (9, 16)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File