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(-) Description

Title :  CRYSTAL STRUCTURE OF WHY2 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 :  1.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Plant, Whirly, 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

(-) Compounds

Molecule 1 - SINGLE-STRANDED DNA-BINDING PROTEIN WHY2, MITOCHONDRIAL
    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 45-212
    Gene: AT1G71260, F3I17.9, WHY2
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: COL-0
    Synonym: PROTEIN WHIRLY 2, ATWHY2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MPO6Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:112 , PHE A:113 , ALA A:114 , HIS A:136 , LYS A:150 , HOH A:453 , SER D:81 , ASN D:83BINDING SITE FOR RESIDUE MPO A 301
2AC2SOFTWAREGLU B:108 , ASP B:159 , SER B:161 , PRO B:183 , HOH B:410BINDING SITE FOR RESIDUE MPO B 301
3AC3SOFTWARELYS B:112 , PHE B:113 , ALA B:114 , HIS B:136 , ASP B:137 , LYS B:150BINDING SITE FOR RESIDUE MPO B 302
4AC4SOFTWAREGLU A:78 , SER A:81 , GLY A:82 , ARG C:103BINDING SITE FOR RESIDUE MPO C 301
5AC5SOFTWARELYS D:112 , PHE D:113 , ALA D:114 , HIS D:136 , LYS D:150BINDING SITE FOR RESIDUE MPO D 301
6AC6SOFTWAREHIS C:157 , PHE C:164 , PRO C:183 , HOH C:484 , LYS D:64 , SER D:166 , VAL D:181BINDING SITE FOR RESIDUE MPO D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser D:81 -Gly D:82
2Asp D:137 -Pro D:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KOP)

(-) Sequences/Alignments

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:154
                                                                                                                                                                                          
               SCOP domains d4kopa_ A: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeeeeeee..eeeeehhhheeeee..eeeeeeeeeee..ee.hhhheeeeehhhhhhhhhh......eeeee...eeeeeeeee.....eeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kop A  53 RLFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALSPTEVGSLISMGSKDSSEFFHDPQVRKSLSVKPHADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRLTGHLE 214
                                    62        72        82        92       102       112       122       132     ||150       160       170       180       190       200       210    
                                                                                                               138|                                                                   
                                                                                                                147                                                                   


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4kopb_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeee...eeeeeeee..eeee.hhh.eeeee..eeeeeeee............eeeeehhhhhhhhhh......eeeee...eeeeeeeee.....eeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kop B  53 RLFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALSPTEVGSLISMGSKDSSEFFHDPQVRKSLSVKPHADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRLTG 211
                                    62        72        82        92       102       112       122       132     ||150       160       170       180       190       200       210 
                                                                                                               138|                                                                
                                                                                                                147                                                                


Chain C from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains d4kopc_ C: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeeeeeee...eee.hhh.eee....eeeeeeeeeee..ee.hhhheeeeehhhhhhhhhh......eeeee.....eeeeeeee.....eeeeeeeee.......eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kop C  53 RLFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALSPTEVGSLISMGSKDSSEFFHDPGQVRKSLSVKPHADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRLTG 211
                                    62        72        82        92       102       112       122       132     ||149       159       169       179       189       199       209  
                                                                                                               138|                                                                 
                                                                                                                146                                                                 


Chain D from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains d4kopd_ D: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...eeeeeeee..eeeeehhhheeeee..eeeeeeeeeee..ee.hhhheeeeehhhhhhhhhh......eeeee...eeeeeeee.....eeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kop D  54 LFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALSPTEVGSLISMGSKDSSEFFHDPVRKSLSVKPHADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTAFSFALPHIMGWN 207
                                    63        73        83        93       103       113       123       133    || 152       162       172       182       192       202     
                                                                                                              138|                                                           
                                                                                                               148
   Legend:   → Mismatch (orange background)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  4kop
    Family and Domain Information: ProDom | SYSTERS
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  WHY2_ARATH | Q8VYF7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

4koo 4koq