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Title :   CRYSTAL STRUCTURE OF POTATO CALMODULIN PCM6

Authors :   D. C. Liang, C. H. Yun, W. R. Chang

Date :   10 Nov 03 (Deposition) - 29 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Plant Calmodulin, Crystal Structure, Pcm6, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. H. Yun, J. Bai, D. Y. Sun, D. F. Cui, W. R. Chang, D. C. Liang
Structure Of Potato Calmodulin Pcm6: The First Report Of The Three-Dimensional Structure Of A Plant Calmodulin.
Acta Crystallogr. , Sect. D V. 60 1214 2004
PubMed-ID: 15213382 | Reference-DOI: 10.1107/S0907444904009771
(for further references see the PDB file header)

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PCM6
	Organism Common	:	POTATO
	Organism Scientific	:	SOLANUM TUBEROSUM
	Organism Taxid	:	4113
	Synonym	:	PCM6

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , CYS A:26 , GLU A:31 , HOH A:4109	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67 , HOH A:4056	BINDING SITE FOR RESIDUE CA A 1002
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , PHE A:99 , GLU A:104 , HOH A:4063	BINDING SITE FOR RESIDUE CA A 1003
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140 , HOH A:4062	BINDING SITE FOR RESIDUE CA A 1004
5	AC5	SOFTWARE	LYS A:86 , PHE A:89 , HOH A:4022	BINDING SITE FOR RESIDUE MPD A 2001
6	AC6	SOFTWARE	LEU A:105 , ALA A:128 , MET A:145	BINDING SITE FOR RESIDUE MPD A 3001
7	AC7	SOFTWARE	PRO A:66 , GLN A:96 , ASP A:122 , ARG A:126 , GLY A:134 , HOH A:4023 , HOH A:4047	BINDING SITE FOR RESIDUE MPD A 4001

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

(no "Cis Peptide Bond" information available for 1RFJ)

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM5_SOLTU	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-147
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM5_SOLTU	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 1RFJ)

Asymmetric/Biological 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:148
 aligned with CALM5_SOLTU | Q7DMN9 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
          CALM5_SOLTU     1 MADQLTEDQISEFKEAFSLFDKDGDGCITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLNLMARKMKDTDSEEELKEAFRVFDKDQNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYDEFVKVMMA 148
               SCOP domains d1rfja_ A: Calmodulin                                                                                                                                SCOP domains
               CATH domains 1rfjA01 A:0-77 EF-hand                                                        1rfjA02 A:78-147 EF-hand                                               CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------EF_hand_5-1rfjA01 A:84-145                                    -- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------EF_hand_5-1rfjA02 A:84-145                                    -- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------EF_hand_6-1rfjA03 A:96-147                           Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------EF_hand_6-1rfjA04 A:96-147                           Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhhhh......eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-147        PROSITE (1)
                PROSITE (2) --------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfj A   0 MADQLTEDQISEFKEAFSLFDKDGDGCITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLNLMARKMKDTDSEEELKEAFRVFDKDQNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYDEFVKVMMA 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with Q42478_SOLCO | Q42478 from UniProtKB/TrEMBL  Length:149

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         Q42478_SOLCO     1 MADQLTEDQISEFKEAFSLFDKDGDGCITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLNLMARKMKDTDSEEELKEAFRVFDKDQNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYDEFVKVMMA 148
               SCOP domains d1rfja_ A: Calmodulin                                                                                                                                SCOP domains
               CATH domains 1rfjA01 A:0-77 EF-hand                                                        1rfjA02 A:78-147 EF-hand                                               CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------EF_hand_5-1rfjA01 A:84-145                                    -- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------EF_hand_5-1rfjA02 A:84-145                                    -- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------EF_hand_6-1rfjA03 A:96-147                           Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------EF_hand_6-1rfjA04 A:96-147                           Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhhhh......eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfj A   0 MADQLTEDQISEFKEAFSLFDKDGDGCITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLNLMARKMKDTDSEEELKEAFRVFDKDQNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYDEFVKVMMA 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Calmodulin (152)

Potato (Solanum tuberosum) [TaxId: 4113] (1)

d1rfja_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Potato (Solanum tuberosum) (1)

1a	1rfjA01	A:0-77
1b	1rfjA02	A:78-147

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Solanum tuberosum (Potato) (1)

1a	EF_hand_5-1rfjA01	A:84-145
1b	EF_hand_5-1rfjA02	A:84-145

Family: EF_hand_6 (75)

Solanum tuberosum (Potato) (1)

2a	EF_hand_6-1rfjA03	A:96-147
2b	EF_hand_6-1rfjA04	A:96-147

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALM5_SOLTU | Q7DMN9)

molecular function
	GO:0005509		calcium ion binding		Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Chain A (Q42478_SOLCO | Q42478)

molecular function
	GO:0005509		calcium ion binding		Interacting selectively and non-covalently with calcium ions (Ca2+).

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 7)

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