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(-) Description

Title :  CRYSTAL STRUCTURE OF A FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN (AVA_3312) FROM ANABAENA VARIABILIS AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  16 Jan 07  (Deposition) - 30 Jan 07  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Xish Protein, Fdxn Element Excision Controlling Factor Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Hwang, J. W. Golden, J. Pascual, D. Xu, A. Cheltsov, A. Godzik
Site-Specific Recombination Of Nitrogen-Fixation Genes In Cyanobacteria By Xisf-Xish-Xisi Complex: Structures And Models.
Proteins 2014
PubMed-ID: 25179344  |  Reference-DOI: 10.1002/PROT.24679

(-) Compounds

Molecule 1 - FDXN ELEMENT EXCISION CONTROLLING FACTOR PROTEIN
    Atcc: 29413
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_323815.1, AVA_3312
    Organism Scientific: ANABAENA VARIABILIS
    Organism Taxid: 1172
    Strain: PCC 7937

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3EDO9Ligand/Ion1,2-ETHANEDIOL
4MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU B:101 , THR B:102 , VAL B:129 , HOH B:184BINDING SITE FOR RESIDUE CL B 140
02AC2SOFTWARELEU A:101 , THR A:102 , VAL A:129 , HOH A:188BINDING SITE FOR RESIDUE CL A 140
03AC3SOFTWARELYS A:16 , LYS A:17 , GLY A:19 , GLU A:119 , GLN A:121 , HOH A:175 , HOH A:208 , HOH A:243BINDING SITE FOR RESIDUE ACT A 141
04AC4SOFTWAREARG A:83 , ARG A:87 , GLN A:121 , HOH A:169 , LYS B:17 , HOH B:208BINDING SITE FOR RESIDUE ACT A 142
05AC5SOFTWAREGLN A:51 , ILE A:117 , GLN A:121 , VAL A:122 , ILE A:138 , ASN A:139 , HOH A:170 , HOH A:178 , HOH A:211BINDING SITE FOR RESIDUE EDO A 143
06AC6SOFTWARELYS A:60 , HOH A:215 , HOH A:261BINDING SITE FOR RESIDUE EDO A 144
07AC7SOFTWARETRP B:20 , GLN B:53 , TYR B:96 , TRP B:137 , ASN B:139 , HOH B:194BINDING SITE FOR RESIDUE EDO B 141
08AC8SOFTWARETRP A:20 , GLN A:53 , TYR A:96 , TRP A:137 , ASN A:139 , HOH A:200 , HOH A:223BINDING SITE FOR RESIDUE EDO A 145
09AC9SOFTWAREGLN B:51 , ILE B:117 , GLN B:121 , VAL B:122 , ILE B:138 , ASN B:139 , HOH B:167 , HOH B:173 , HOH B:225BINDING SITE FOR RESIDUE EDO B 142
10BC1SOFTWAREGLN A:78 , HOH A:172 , SER B:70 , HIS B:73 , HOH B:231BINDING SITE FOR RESIDUE EDO A 146
11BC2SOFTWARESER A:70 , HIS A:73 , HOH A:173 , HOH A:249 , GLN B:78BINDING SITE FOR RESIDUE EDO A 147
12BC3SOFTWARELYS A:88 , ASP B:111 , PHE B:112 , GLU B:115 , HOH B:226 , HOH B:281BINDING SITE FOR RESIDUE EDO B 143
13BC4SOFTWAREASP A:111 , PHE A:112 , GLU A:115 , HOH A:233 , LYS B:88BINDING SITE FOR RESIDUE EDO A 148

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:25 -Pro A:26
2Asp B:25 -Pro B:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OKF)

(-) Exons   (0, 0)

(no "Exon" information available for 2OKF)

(-) 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:129
 aligned with Q3M7W6_ANAVT | Q3M7W6 from UniProtKB/TrEMBL  Length:139

    Alignment length:136
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      
         Q3M7W6_ANAVT     4 RDVFHEVVKTALKKDGWQITDDPLTISVGGVNLSIDLAAQKLIAAERQGQKIAVEVKSFLKQSSAISEFHTALGQFINYRGALRKVEPDRVLYLAVPLTTYKTFFQLDFPKEIIIENQVKMLVYDVEQEVIFQWIN 139
               SCOP domains d2okfa1 A:4-139 FdxN element exci       sion controlling factor protein                                                                  SCOP domains
               CATH domains 2okfA00 A:4-139  [code=3.40.1350.       10, no name defined]                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeee.....ee..ee.-------..eeeee..eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhh...eeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okf A   4 RDVFHEVVKTALKKDGWQITDDPLTISVGGVNL-------KLIAAERQGQKIAVEVKSFLKQSSAISEFHTALGQFINYRGALRKVEPDRVLYLAVPLTTYKTFFQLDFPKEIIIENQVKmLVYDVEQEVIFQWIN 139
                                    13        23        33  |      -|       53        63        73        83        93       103       113       123|      133      
                                                           36      44                                                                             124-MSE           


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q3M7W6_ANAVT | Q3M7W6 from UniProtKB/TrEMBL  Length:139

    Alignment length:136
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      
         Q3M7W6_ANAVT     4 RDVFHEVVKTALKKDGWQITDDPLTISVGGVNLSIDLAAQKLIAAERQGQKIAVEVKSFLKQSSAISEFHTALGQFINYRGALRKVEPDRVLYLAVPLTTYKTFFQLDFPKEIIIENQVKMLVYDVEQEVIFQWIN 139
               SCOP domains d2okfb_ B: FdxN element excision        controlling factor protein                                                                       SCOP domains
               CATH domains 2okfB00 B:4-139  [code=3.40.1350.       10, no name defined]                                                                             CATH domains
           Pfam domains (1) XisH-2okfB01 B:4-136                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) XisH-2okfB02 B:4-136                                                                                                                 --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh..eeee.....ee..ee.-------..eeeee..eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhh...eeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okf B   4 RDVFHEVVKTALKKDGWQITDDPLTISVGGVNL-------KLIAAERQGQKIAVEVKSFLKQSSAISEFHTALGQFINYRGALRKVEPDRVLYLAVPLTTYKTFFQLDFPKEIIIENQVKmLVYDVEQEVIFQWIN 139
                                    13        23        33  |      -|       53        63        73        83        93       103       113       123|      133      
                                                           36      44                                                                             124-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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PDDEXK (13)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3M7W6_ANAVT | Q3M7W6)
molecular function
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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