2Q41 - JenaLib

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Title :   ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA GENE AT1G23820

Authors :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)

Date :   31 May 07 (Deposition) - 19 Jun 07 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D  (8x)
Biol. Unit 1: A,B,C,D  (1x)

Keywords :   Ensemble Refinement, Refinement Methodology Development, At1G23820, Putrescine Aminopropyl Transferase, Spermidine Synthase, Spds1, Polyamine, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744 | Reference-DOI: 10.1016/J.STR.2007.06.019

Molecule 1 - SPERMIDINE SYNTHASE 1
	Chains	:	A, B, C, D
	EC Number	:	2.5.1.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP-16
	Expression System Strain	:	PLACI+RARE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SPDSYN1, AT1G23820, F5O8.38
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Strain	:	CV. COLUMBIA
	Synonym	:	PUTRESCINE AMINOPROPYLTRANSFERASE 1, SPDSY 1

		1	2	3	4
Asymmetric Unit (8x)	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 28)

No.	Name	Count	Type	Full Name
1	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 28)

No.	Name	Count	Type	Full Name
1	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2Q41)

(no "SS Bond" information available for 2Q41)

(no "Cis Peptide Bond" information available for 2Q41)

(no "SAP(SNP)/Variant" information available for 2Q41)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPD1_ARATH	45-282	4	A:45-282 B:45-282 C:45-282 D:45-282
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPD1_ARATH	124-137	4	A:124-137 B:124-137 C:124-137 D:124-137

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPD1_ARATH	45-282	4	A:45-282 B:45-282 C:45-282 D:45-282
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPD1_ARATH	124-137	4	A:124-137 B:124-137 C:124-137 D:124-137

(no "Exon" information available for 2Q41)

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:290
 aligned with SPD1_ARATH | Q9ZUB3 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:290
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
           SPD1_ARATH    41 STVIPGWFSEMSPMWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEMITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHMDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFMLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIE 330
               SCOP domains d2q41a_ A: Spermidine synthase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------2q41A02 A:98-330 Vaccinia Virus protein VP39                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeee....hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhh.....eeeeeee.......eeeeeeee...................hhhhh.....hhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PABS_2  PDB: A:45-282 UniProt: 45-282                                                                                                                                                                                                         ------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q41 A  41 STVIPGWFSEmSPmWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEmITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDmCEIDKmVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHmDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFmLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIE 330
                                    50|  |    60        70        80        90       100       110       120       130       140       150    |  160       170       180       190       200       210       220       230       240 |     250       260       270       280       290       300       310       320       330
                                     51-MSE                                                   109-MSE                                 149-MSE |                                                                                    242-MSE                             278-MSE                                                
                                        54-MSE                                                                                              155-MSE

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with SPD1_ARATH | Q9ZUB3 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:293
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327   
           SPD1_ARATH    38 ACFSTVIPGWFSEMSPMWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEMITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHMDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFMLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIE 330
               SCOP domains d2q41b_ B: Spermidine synthase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------2q41B02 B:98-330 Vaccinia Virus protein VP39                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeee....hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhheeeeeeeeee........hhhhhhhhhhhhhh...eeeeeee...hhh.eeeeeeee...............--------......hhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PABS_2  PDB: B:45-282 UniProt: 45-282                                                                                                                                                                                                         ------------------------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q41 B  38 ACFSTVIPGWFSEmSPmWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEmITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDmCEIDKmVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHmDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFmLCSTEGPDVDFKHPLNPI--------GPLKFYNAEIHSAAFCLPSFAKKVIE 330
                                    47   |  | 57        67        77        87        97       107 |     117       127       137       147 |     157       167       177       187       197       207       217       227       237    |  247       257       267       277|      287        |-       307       317       327   
                                        51-MSE                                                   109-MSE                                 149-MSE |                                                                                    242-MSE                             278-MSE           296      305                         
                                           54-MSE                                                                                              155-MSE

Chain C from PDB  Type:PROTEIN  Length:290
 aligned with SPD1_ARATH | Q9ZUB3 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:290
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
           SPD1_ARATH    41 STVIPGWFSEMSPMWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEMITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHMDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFMLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIE 330
               SCOP domains d2q41c_ C: Spermidine synthase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------2q41C02 C:98-330 Vaccinia Virus protein VP39                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeee....hhhhhhhhh.....eeeeee.hhhhhhhhhhhh...hhhhhh..eeeee.....hhhhh....eeeeee......hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh...eeeeeee.......eeeeeeee................hhhhhhhh.....hhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PABS_2  PDB: C:45-282 UniProt: 45-282                                                                                                                                                                                                         ------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q41 C  41 STVIPGWFSEmSPmWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEmITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDmCEIDKmVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHmDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFmLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIE 330
                                    50|  |    60        70        80        90       100       110       120       130       140       150    |  160       170       180       190       200       210       220       230       240 |     250       260       270       280       290       300       310       320       330
                                     51-MSE                                                   109-MSE                                 149-MSE |                                                                                    242-MSE                             278-MSE                                                
                                        54-MSE                                                                                              155-MSE

Chain D from PDB  Type:PROTEIN  Length:285
 aligned with SPD1_ARATH | Q9ZUB3 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:293
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327   
           SPD1_ARATH    38 ACFSTVIPGWFSEMSPMWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEMITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDMCEIDKMVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHMDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFMLCSTEGPDVDFKHPLNPIDESSSKSNGPLKFYNAEIHSAAFCLPSFAKKVIE 330
               SCOP domains d2q41d_ D: Spermidine synthase                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------2q41D02 D:98-330 Vaccinia Virus protein VP39                                                                                                                                                                                              CATH domains
           Pfam domains (1) --------Spermine_synth-2q41D01 D:46-291                                                                                                                                                                                                                       --------------------------------------- Pfam domains (1)
           Pfam domains (2) --------Spermine_synth-2q41D02 D:46-291                                                                                                                                                                                                                       --------------------------------------- Pfam domains (2)
           Pfam domains (3) --------Spermine_synth-2q41D03 D:46-291                                                                                                                                                                                                                       --------------------------------------- Pfam domains (3)
           Pfam domains (4) --------Spermine_synth-2q41D04 D:46-291                                                                                                                                                                                                                       --------------------------------------- Pfam domains (4)
         Sec.struct. author .........eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhh..hhhhh....eeeee.hhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhhhheeeeeeeeee......hhhhhhhhhhhhhhhh...eeeeeee...hhh.eeeeeeee...............--------......hhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PABS_2  PDB: D:45-282 UniProt: 45-282                                                                                                                                                                                                         ------------------------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q41 D  38 ACFSTVIPGWFSEmSPmWPGEAHSLKVEKVLFQGKSDYQDVIVFQSATYGKVLVLDGVIQLTERDECAYQEmITHLPLCSIPNPKKVLVIGGGDGGVLREVARHASIEQIDmCEIDKmVVDVSKQFFPDVAIGYEDPRVNLVIGDGVAFLKNAAEGSYDAVIVDSSDPIGPAKELFEKPFFQSVARALRPGGVVCTQAESLWLHmDIIEDIVSNCREIFKGSVNYAWTSVPTYPSGVIGFmLCSTEGPDVDFKHPLNPI--------GPLKFYNAEIHSAAFCLPSFAKKVIE 330
                                    47   |  | 57        67        77        87        97       107 |     117       127       137       147 |     157       167       177       187       197       207       217       227       237    |  247       257       267       277|      287        |-       307       317       327   
                                        51-MSE                                                   109-MSE                                 149-MSE |                                                                                    242-MSE                             278-MSE           296      305                         
                                           54-MSE                                                                                              155-MSE

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Spermidine synthase (17)

Protein domain: Spermidine synthase (11)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (2)

1a	d2q41a_	A:
1b	d2q41b_	B:
1c	d2q41c_	C:
1d	d2q41d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Thale cress (Arabidopsis thaliana) (2)

1a	2q41B02	B:98-330
1b	2q41D02	D:98-330
1c	2q41A02	A:98-330
1d	2q41C02	C:98-330

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Spermine_synth (12)

Arabidopsis thaliana (Mouse-ear cress) (2)

1a	Spermine_synth-2q41D01	D:46-291
1b	Spermine_synth-2q41D02	D:46-291
1c	Spermine_synth-2q41D03	D:46-291
1d	Spermine_synth-2q41D04	D:46-291

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SPD1_ARATH | Q9ZUB3)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004766	spermidine synthase activity	Catalysis of the reaction: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006596	polyamine biosynthetic process	The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
	GO:0006595	polyamine metabolic process	The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.
	GO:0008295	spermidine biosynthetic process	The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.

Asymmetric Unit
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Biological Unit
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	2q41
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	SPD1_ARATH \| Q9ZUB3	:	1xj5

1xj5	ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.

Description

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Ligands, Modified Residues, Ions (1, 28)

Sites (0, 0)

SS Bonds (0, 0)

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