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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE ENDORIBONUCLEASE L-PSP FROM ENTAMOEBA HISTOLYTICA WITH HIGHER SOLVENT CONTENT AND AN ORDERED N-TERMINAL TAG
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  28 Apr 10  (Deposition) - 12 May 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Putative Endoribonuclease, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gardberg, J. Abendroth, B. Staker
Crystal Structure Of A Putative Endoribonuclease L-Psp From Entamoeba Histolytica
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ENDORIBONUCLEASE L-PSP
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1FLC5Ligand/IonCITRATE ANION
2GOL6Ligand/IonGLYCEROL
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1FLC3Ligand/IonCITRATE ANION
2GOL3Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2GOL3Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:19 , GLY A:33 , ILE A:35 , PRO A:114 , LYS A:115 , GLU A:120 , HOH A:446 , HOH A:592 , ARG C:105 , ALA C:106 , CYS C:107BINDING SITE FOR RESIDUE FLC A 140
02AC2SOFTWARELYS A:76 , THR A:77 , THR A:78 , HOH A:473 , GOL B:145 , GOL C:145BINDING SITE FOR RESIDUE GOL A 145
03AC3SOFTWAREARG A:105 , ALA A:106 , CYS A:107 , TYR B:19 , GLY B:33 , PRO B:114 , LYS B:115 , GLU B:120 , HOH B:146 , HOH B:558BINDING SITE FOR RESIDUE FLC B 140
04AC4SOFTWARELYS B:73 , HOH B:613 , LYS C:3 , LYS D:73BINDING SITE FOR RESIDUE SO4 B 150
05AC5SOFTWAREARG B:39 , HOH B:681BINDING SITE FOR RESIDUE SO4 B 155
06AC6SOFTWAREGOL A:145 , LYS B:76 , THR B:77 , THR B:78 , GLU B:122 , CYS B:123 , HOH B:634 , GOL C:145BINDING SITE FOR RESIDUE GOL B 145
07AC7SOFTWAREPHE B:87 , ARG B:105 , ALA B:106 , CYS B:107 , TYR C:19 , GLY C:33 , ILE C:35 , PRO C:114 , LYS C:115 , GLU C:120 , HOH C:686 , HOH C:769BINDING SITE FOR RESIDUE FLC C 140
08AC8SOFTWARELYS C:73 , LYS F:73BINDING SITE FOR RESIDUE SO4 C 150
09AC9SOFTWAREVAL B:16 , GLY B:17 , TYR B:19 , LYS B:115 , HOH B:359 , HOH B:601 , ARG C:39 , HOH C:462 , HOH C:745BINDING SITE FOR RESIDUE SO4 C 155
10BC1SOFTWAREGOL A:145 , GOL B:145 , HOH B:634 , LYS C:76 , THR C:77 , THR C:78 , GLU C:122 , ILE C:124 , HOH C:157BINDING SITE FOR RESIDUE GOL C 145
11BC2SOFTWARETYR D:19 , GLY D:33 , PRO D:114 , LYS D:115 , GLU D:120 , HOH D:593 , HOH D:607 , PHE F:87 , ARG F:105 , ALA F:106 , CYS F:107BINDING SITE FOR RESIDUE FLC D 140
12BC3SOFTWAREARG D:39 , HOH D:509 , HOH D:618BINDING SITE FOR RESIDUE SO4 D 155
13BC4SOFTWARELYS D:76 , THR D:77 , THR D:78 , GLU D:122 , ILE D:124 , HOH D:676 , GOL E:145 , HOH E:651 , GOL F:145BINDING SITE FOR RESIDUE GOL D 145
14BC5SOFTWARELYS A:73 , LYS B:3 , LYS E:73BINDING SITE FOR RESIDUE SO4 E 150
15BC6SOFTWAREPHE D:87 , ARG D:105 , ALA D:106 , CYS D:107 , TYR E:19 , GLY E:33 , PRO E:114 , LYS E:115 , GLU E:120 , HOH E:481 , HOH E:606BINDING SITE FOR RESIDUE FLC E 140
16BC7SOFTWAREGOL D:145 , LYS E:76 , THR E:77 , THR E:78 , GLU E:122 , ILE E:124 , HOH E:416 , HOH E:651 , GOL F:145BINDING SITE FOR RESIDUE GOL E 145
17BC8SOFTWAREARG F:39BINDING SITE FOR RESIDUE SO4 F 155
18BC9SOFTWAREGOL D:145 , GOL E:145 , LYS F:76 , THR F:77 , THR F:78 , CYS F:123 , ILE F:124BINDING SITE FOR RESIDUE GOL F 145

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MQW)

(-) 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:132
 aligned with C4LXT9_ENTHI | C4LXT9 from UniProtKB/TrEMBL  Length:127

    Alignment length:132
                                 1                                                                                                                              
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125  
         C4LXT9_ENTHI     - -----MSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
               SCOP domains d3mqwa_ A: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhhh....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mqw A  -6 QTQGPMSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125  
                               -2|                                                                                                                              
                                 1                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with C4LXT9_ENTHI | C4LXT9 from UniProtKB/TrEMBL  Length:127

    Alignment length:140
                                         1                                                                                                                              
                                     -   |     7        17        27        37        47        57        67        77        87        97       107       117       127
         C4LXT9_ENTHI     - -------------MSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
               SCOP domains d3mqwb_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhhh....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqw B -12 MGTLEAQTQGPGSMSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
                                    -3         7        17        27        37        47        57        67        77        87        97       107       117       127


Chain C from PDB  Type:PROTEIN  Length:136
 aligned with C4LXT9_ENTHI | C4LXT9 from UniProtKB/TrEMBL  Length:127

    Alignment length:136
                                     1                                                                                                                              
                                     1        11        21        31        41        51        61        71        81        91       101       111       121      
         C4LXT9_ENTHI     - ---------MSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
               SCOP domains d3mqwc_ C: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhhh....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqw C  -8 EAQTQGPGSMSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
                                     1        11        21        31        41        51        61        71        81        91       101       111       121      


Chain D from PDB  Type:PROTEIN  Length:141
 aligned with C4LXT9_ENTHI | C4LXT9 from UniProtKB/TrEMBL  Length:127

    Alignment length:141
                                          1                                                                                                                              
                                     -    |    6        16        26        36        46        56        66        76        86        96       106       116       126 
         C4LXT9_ENTHI     - --------------MSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
               SCOP domains d3mqwd_ D: automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.hhhhhhhhhhhhhhhhh....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqw D -13 HMGTLEAQTQGPGSMSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
                                    -4         6        16        26        36        46        56        66        76        86        96       106       116       126 


Chain E from PDB  Type:PROTEIN  Length:135
 aligned with C4LXT9_ENTHI | C4LXT9 from UniProtKB/TrEMBL  Length:127

    Alignment length:135
                                    1                                                                                                                              
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122     
         C4LXT9_ENTHI     - --------MSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
               SCOP domains d3mqwe_ E: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee..............eeee..eeeeeee.............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhhh....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqw E  -7 AQTQGPGSMSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
                                     2        12        22        32        42        52        62        72        82        92       102       112       122     


Chain F from PDB  Type:PROTEIN  Length:133
 aligned with C4LXT9_ENTHI | C4LXT9 from UniProtKB/TrEMBL  Length:127

    Alignment length:133
                                  1                                                                                                                              
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124   
         C4LXT9_ENTHI     - ------MSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
               SCOP domains d3mqwf_ F: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Ribonuc_L-PSP-3mqwF01 F:9-127                                                                                           Pfam domains (1)
           Pfam domains (2) --------------Ribonuc_L-PSP-3mqwF02 F:9-127                                                                                           Pfam domains (2)
           Pfam domains (3) --------------Ribonuc_L-PSP-3mqwF03 F:9-127                                                                                           Pfam domains (3)
           Pfam domains (4) --------------Ribonuc_L-PSP-3mqwF04 F:9-127                                                                                           Pfam domains (4)
           Pfam domains (5) --------------Ribonuc_L-PSP-3mqwF05 F:9-127                                                                                           Pfam domains (5)
           Pfam domains (6) --------------Ribonuc_L-PSP-3mqwF06 F:9-127                                                                                           Pfam domains (6)
         Sec.struct. author .........eeee..............eeee..eeeeeeee............hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.hhhhhhhhhhhhhhhhh....eeeeee...hhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqw F  -7 AQTQGPMSKLTVVASPLAPEAVGAYSQAIICNGMVYCSGQIGLDRKTGDFAGKTIEEQSKQVMTNLKYVLEEAGSSMDKVVKTTCLLADIKDFGVFNGIYAEAFGNHKPARACFAAAALPKGALVEVECIATL 127
                                 ||  4        14        24        34        44        54        64        74        84        94       104       114       124   
                                -2|                                                                                                                              
                                  1
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  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 3MQW)

(-) 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 3MQW)

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  3mqw
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 Related Entries

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

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        C4LXT9_ENTHI | C4LXT9: 3m1x 3m4s

(-) Related Entries Specified in the PDB File

3m1x 3m4s