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(-) Description

Title :  CRYSTAL STRUCTURE OF L-PSP PUTATIVE ENDORIBONUCLEASE FROM UNCULTURED ORGANISM
 
Authors :  M. E. Cuff, P. Petit, X. Xu, H. Cui, A. Savchenko, A. F. Yakunin
Date :  08 Mar 11  (Deposition) - 23 Mar 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  C,D,E  (1x)
Biol. Unit 3:  A,B,C,D,E,F  (1x)
Keywords :  Endoribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, P. Petit, X. Xu, H. Cui, A. Savchenko, A. F. Yakunin
Crystal Structure Of L-Psp Putative Endoribonuclease From Uncultured Organism
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-PSP PUTATIVE ENDORIBONUCLEASE
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: UNCULTURED ORGANISM
    Organism Taxid: 155900

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB   F
Biological Unit 2 (1x):   CDE 
Biological Unit 3 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3R0P)

(-) Sites  (0, 0)

(no "Site" information available for 3R0P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R0P)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:100 -Pro A:101
2Ala B:100 -Pro B:101
3Ala C:100 -Pro C:101
4Ala D:100 -Pro D:101
5Ala E:100 -Pro E:101
6Ala F:100 -Pro F:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R0P)

(-) Exons   (0, 0)

(no "Exon" information available for 3R0P)

(-) 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    
   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:125
 aligned with D8VN48_9ZZZZ | D8VN48 from UniProtKB/TrEMBL  Length:127

    Alignment length:125
                                    12        22        32        42        52        62        72        82        92       102       112       122     
         D8VN48_9ZZZZ     3 NKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
               SCOP domains d3r0pa_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0p A   3 NKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
                                    12        22        32        42        52        62        72        82        92       102       112       122     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with D8VN48_9ZZZZ | D8VN48 from UniProtKB/TrEMBL  Length:127

    Alignment length:125
                                    12        22        32        42        52        62        72        82        92       102       112       122     
         D8VN48_9ZZZZ     3 NKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
               SCOP domains d3r0pb_ B: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0p B   3 NKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
                                    12        22        32        42        52        62        72        82        92       102       112       122     


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with D8VN48_9ZZZZ | D8VN48 from UniProtKB/TrEMBL  Length:127

    Alignment length:127
                                    10        20        30        40        50        60        70        80        90       100       110       120       
         D8VN48_9ZZZZ     1 MTNKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
               SCOP domains d3r0pc_ C: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..............eeee..eeeeeee..ee....ee...hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0p C   1 MTNKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
                                    10        20        30        40        50        60        70        80        90       100       110       120       


Chain D from PDB  Type:PROTEIN  Length:126
 aligned with D8VN48_9ZZZZ | D8VN48 from UniProtKB/TrEMBL  Length:127

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
         D8VN48_9ZZZZ     2 TNKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
               SCOP domains d3r0pd_ D: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r0p D   2 TNKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
                                    11        21        31        41        51        61        71        81        91       101       111       121      


Chain E from PDB  Type:PROTEIN  Length:125
 aligned with D8VN48_9ZZZZ | D8VN48 from UniProtKB/TrEMBL  Length:127

    Alignment length:125
                                    12        22        32        42        52        62        72        82        92       102       112       122     
         D8VN48_9ZZZZ     3 NKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
               SCOP domains d3r0pe_ E: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..............eeee..eeeeeee..ee....ee...hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r0p E   3 NKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
                                    12        22        32        42        52        62        72        82        92       102       112       122     


Chain F from PDB  Type:PROTEIN  Length:126
 aligned with D8VN48_9ZZZZ | D8VN48 from UniProtKB/TrEMBL  Length:127

    Alignment length:126
                                    11        21        31        41        51        61        71        81        91       101       111       121      
         D8VN48_9ZZZZ     2 TNKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
               SCOP domains d3r0pf_ F: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------Ribonuc_L-PSP-3r0pF01 F:9-127                                                                                           Pfam domains (1)
           Pfam domains (2) -------Ribonuc_L-PSP-3r0pF02 F:9-127                                                                                           Pfam domains (2)
           Pfam domains (3) -------Ribonuc_L-PSP-3r0pF03 F:9-127                                                                                           Pfam domains (3)
           Pfam domains (4) -------Ribonuc_L-PSP-3r0pF04 F:9-127                                                                                           Pfam domains (4)
           Pfam domains (5) -------Ribonuc_L-PSP-3r0pF05 F:9-127                                                                                           Pfam domains (5)
           Pfam domains (6) -------Ribonuc_L-PSP-3r0pF06 F:9-127                                                                                           Pfam domains (6)
         Sec.struct. author ..eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhh........eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r0p F   2 TNKAIIHSDNAPAAIGTYSQAVKVNNTVYLSGQIPLDPVTMQLVEGDFAVQAHQVFKNLRAVCEAAGGGLRDIVKLNVYLTDLANFPIVNEVMGQYFQAPYPARAAIGINQLPRASLIEADGIMVI 127
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R0P)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ribonuc_L-PSP] (16)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3R0P)

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  Cis Peptide Bonds
    Ala A:100 - Pro A:101   [ RasMol ]  
    Ala B:100 - Pro B:101   [ RasMol ]  
    Ala C:100 - Pro C:101   [ RasMol ]  
    Ala D:100 - Pro D:101   [ RasMol ]  
    Ala E:100 - Pro E:101   [ RasMol ]  
    Ala F:100 - Pro F:101   [ RasMol ]  
 
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 Related Entries

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(-) Related Entries Specified in the PDB File

3k0t PSP PROTEIN IN COMPLEX WITH D-BETA-GLUCOSE FROM PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000