4KOO - JenaLib

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Title :   CRYSTAL STRUCTURE OF WHY1 FROM ARABIDOPSIS THALIANA

Authors :   L. Cappadocia, J. S. Parent, N. Brisson, J. Sygusch

Date :   12 May 13 (Deposition) - 13 Nov 13 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: C,D  (2x)

Keywords :   Plant, Whirly, Single-Stranded Dna Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Cappadocia, J. S. Parent, J. Sygusch, N. Brisson
A Family Portrait: Structural Comparison Of The Whirly Proteins From Arabidopsis Thaliana And Solanum Tuberosum.
Acta Crystallogr. , Sect. F V. 69 1207 2013
PubMed-ID: 24192350 | Reference-DOI: 10.1107/S1744309113028698

Molecule 1 - SINGLE-STRANDED DNA-BINDING PROTEIN WHY1, CHLOROPLASTIC
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 74-241
	Gene	:	AT1G14410, F14L17.18, PTAC1, WHY1
	Organism Common	:	MOUSE-EAR CRESS,THALE-CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Strain	:	COL-0
	Synonym	:	PROTEIN PLASTID TRANSCRIPTIONALLY ACTIVE 1, PROTEIN WHIRLY 1, ATWHY1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MES	6	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	NI	1	Ligand/Ion	NICKEL (II) ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MES	6	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MES	6	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:130 , GLN A:131 , TYR A:132 , TRP A:134	BINDING SITE FOR RESIDUE MES A 301
2	AC2	SOFTWARE	PHE A:140 , SER A:141 , HIS A:163 , ASP A:164 , PRO A:165 , LYS A:177 , HOH A:432 , HOH A:443 , HOH A:505	BINDING SITE FOR RESIDUE MES A 302
3	AC3	SOFTWARE	HIS A:248 , HIS A:250 , HOH A:551 , HIS D:248 , HIS D:250	BINDING SITE FOR RESIDUE NI A 303
4	AC4	SOFTWARE	ARG B:130 , GLN B:131 , TYR B:132 , TRP B:134	BINDING SITE FOR RESIDUE MES B 301
5	AC5	SOFTWARE	PHE B:140 , SER B:141 , HIS B:163 , PRO B:165 , LYS B:177 , HOH B:559	BINDING SITE FOR RESIDUE PO4 B 302
6	AC6	SOFTWARE	PHE C:140 , SER C:141 , HIS C:163 , PRO C:165 , LYS C:177	BINDING SITE FOR RESIDUE MES C 301
7	AC7	SOFTWARE	ARG D:130 , TYR D:132 , TRP D:134 , HOH D:491	BINDING SITE FOR RESIDUE MES D 301
8	AC8	SOFTWARE	VAL D:139 , PHE D:140 , SER D:141 , HIS D:163 , PRO D:165 , LYS D:177 , HOH D:437 , HOH D:512	BINDING SITE FOR RESIDUE MES D 302

(no "SS Bond" information available for 4KOO)

(no "Cis Peptide Bond" information available for 4KOO)

(no "SAP(SNP)/Variant" information available for 4KOO)

(no "PROSITE Motif" information available for 4KOO)

(no "Exon" information available for 4KOO)

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:176
                                                                                                                                                                                                                
               SCOP domains d4kooa_ A: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..eeee...eeeeeeee..eeee.....eeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4koo A  77 LPARFYVGHSIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAEFAVLISAFNFVLPYLIGWHAFANSIKAAALEHHHHHH 252
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246

Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains d4koob_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee...eeeeeeee..eeee.....eeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhhh.....eeeee...........eeeeeeeee......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4koo B  78 PARFYVGHSIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAEFAVLISAFNFVLPYLIGWHAFANS 239
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

Chain C from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains d4kooc_ C: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeee...eeeeeeee..eeee.....eeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4koo C  78 PARFYVGHSIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAEFAVLISAFNFVLPYLIGWHAFANSIKA 242
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains d4kood_ D: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...eeeeeeee..eeee.....eeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhhh.....eeeee...........eeeeeeeee......eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4koo D  77 LPARFYVGHSIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAEFAVLISAFNFVLPYLIGWHAFANSIKAAALEHHHHH 251
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: ssDNA-binding transcriptional regulator domain (23)

Superfamily: ssDNA-binding transcriptional regulator domain (23)

Family: Plant transcriptional regulator PBF-2 (3)

Protein domain: automated matches (2)

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

1a	d4kooa_	A:
1b	d4koob_	B:
1c	d4kooc_	C:
1d	d4kood_	D:

(no "CATH Domain" information available for 4KOO)

(no "Pfam Domain" information available for 4KOO)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4koo)

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4koo
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (14, 14)

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