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(-) Description

Title :  MN2+-GMP COMPLEX OF NANORNASE (NRN) FROM BACTEROIDES FRAGILIS
 
Authors :  Y. Uemura, N. Nakagawa, T. Wakamatsu, G. T. Montelione, J. F. Hunt, R. Ma S. Kuramitsu
Date :  07 Feb 13  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dhh Phosphatase, Dhha1 Motif, Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Uemura, N. Nakagawa, T. Wakamatsu, K. Kim, G. T. Montelione, J. F. Hunt, S. Kuramitsu, R. Masui
Crystal Structure Of The Ligand-Binding Form Of Nanornase From Bacteroides Fragilis, A Member Of The Dhh/Dhha1 Phosphoesterase Family Of Proteins
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE EXOPOLYPHOSPHATASE-RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21D
    Expression System Strain: ROSETTA2(DE3)PLYSE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BF3900
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 295405
    Strain: YCH46

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , LYS A:287 , SER A:289 , ARG A:291 , GLY A:308 , GLY A:309 , SER A:315 , GLY A:316 , GLY A:317BINDING SITE FOR RESIDUE 5GP A 401
2AC2SOFTWAREHIS A:29 , ASP A:33 , ASP A:99 , MN A:403BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREASP A:35 , ASP A:99 , HIS A:125 , ASP A:177 , MN A:402BINDING SITE FOR RESIDUE MN A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W5W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W5W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3W5W)

(-) Sequences/Alignments

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    
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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:340
 aligned with Q64PD9_BACFR | Q64PD9 from UniProtKB/TrEMBL  Length:343

    Alignment length:342
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341  
         Q64PD9_BACFR     2 LTKVIAQAHIDHFTKWFERADKIVIVSHVSPDGDAIGSSLGLYHFLDSQDKIVNVIVPNAFPDFLKWMPGSKDILLYDRYQEFADKLIMEADVICCLDFNALKRIDEMSDIVAASPGRKIMIDHHLYPEDFCRITISHPEISSTSELVFRLICRMGYFSDISKEGAECIYTGMMTDTGGFTYNSNNREIYFIISELLSKGIDKDDIYRKVYNTYSESRLRLMGYVLSNMKVYKDYNSALISLTKEEQGKFDYIKGDSEGFVNIPLSIKNVCFSCFLREDTEKKMIKISLRSVGKFPCNRLAAEFFNGGGHLNASGGEFYGTMEEAVKVFEQALEKYKPLLKE 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee....hhhhh...hhhhheehhhhhhhhhhhhhhh.eeeee...hhhhhh.hhhhhhhh..eeeeee..........eeee.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhheeehhh.eeeeeehhhhhhhh...........hhhhhh....eeeeeee...--.eeeeeee....hhhhhhhh....ee...eeeeee..hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3w5w A   2 LTKVIAQAHIDHFTKWFERADKIVIVSHVSPDGDAIGSSLGLYHFLDSQDKIVNVIVPNAFPDFLKWMPGSKDILLYDRYQEFADKLIMEADVICCLDFNALKRIDEMSDIVAASPGRKIMIDHHLYPEDFCRITISHPEISSTSELVFRLICRMGYFSDISKEGAECIYTGMMTDTGGFTYNSNNREIYFIISELLSKGIDKDDIYRKVYNTYSESRLRLMGYVLSNMKVYKDYNSALISLTKEEQGKFDYIKGDSEGFVNIPLSIKNVCFSCFLREDTE--MIKISLRSVGKFPCNRLAAEFFNGGGHLNASGGEFYGTMEEAVKVFEQALEKYKPLLKE 343
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281|  |   291       301       311       321       331       341  
                                                                                                                                                                                                                                                                                                                  282  |                                                          
                                                                                                                                                                                                                                                                                                                     285
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3W5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W5W)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q64PD9_BACFR | Q64PD9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        Q64PD9_BACFR | Q64PD9: 4py9

(-) Related Entries Specified in the PDB File

3dma