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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM S23 RIBOSOMAL PROTEIN FAMILY (BT_0352) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Oct 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uncharacterized Protein (Np_809265. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Atcc: 29148
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_809265.1, BT_0352
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186
    Strain: VPI-5482, DSM 2079, NCTC 10582, E50

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 31)

Asymmetric/Biological Unit (4, 31)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3EDO16Ligand/Ion1,2-ETHANEDIOL
4MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:131 , ASP D:102 , HOH D:130 , HOH D:142 , HOH D:152 , HOH D:160 , HOH D:169 , HOH D:187BINDING SITE FOR RESIDUE CA D 121
02AC2SOFTWAREASP A:4 , ASP A:7 , ASN A:8 , HOH A:157 , HOH A:165 , HOH A:196BINDING SITE FOR RESIDUE CA A 121
03AC3SOFTWAREASP C:4 , ASP C:7 , ASN C:8 , HOH C:190 , HOH C:200BINDING SITE FOR RESIDUE CA C 121
04AC4SOFTWAREPHE A:35 , EDO B:125BINDING SITE FOR RESIDUE CL A 122
05AC5SOFTWAREHOH C:125 , PHE D:35 , HOH D:175BINDING SITE FOR RESIDUE CL D 122
06AC6SOFTWAREARG A:2 , GLU A:3 , ASP A:4 , LYS B:33 , HOH E:144BINDING SITE FOR RESIDUE EDO B 121
07AC7SOFTWAREARG A:20 , GLN A:95 , SER A:98 , HOH A:188BINDING SITE FOR RESIDUE EDO A 123
08AC8SOFTWARETHR C:46 , SER C:47 , ALA C:50 , GLU D:77 , TRP D:81BINDING SITE FOR RESIDUE EDO C 122
09AC9SOFTWAREASN C:23 , GLN C:95 , HOH C:151BINDING SITE FOR RESIDUE EDO C 123
10BC1SOFTWARELYS B:39 , HOH B:135 , HOH B:182 , TYR E:25 , LEU E:42BINDING SITE FOR RESIDUE EDO B 122
11BC2SOFTWAREGLY A:0 , MSE A:1 , GLU A:3 , LYS A:6 , GLN B:32BINDING SITE FOR RESIDUE EDO A 124
12BC3SOFTWARETYR A:90 , HOH A:130 , VAL B:22 , ASN B:23 , LYS B:26 , HOH B:189BINDING SITE FOR RESIDUE EDO B 123
13BC4SOFTWARELYS A:26 , HOH A:209 , THR C:88 , GLU C:89BINDING SITE FOR RESIDUE EDO A 125
14BC5SOFTWAREARG B:20 , ASN B:23 , HOH B:153 , HOH B:184 , ARG D:93 , HOH D:227BINDING SITE FOR RESIDUE EDO B 124
15BC6SOFTWAREARG E:93 , GLU E:97 , HOH E:202BINDING SITE FOR RESIDUE EDO E 121
16BC7SOFTWAREASN A:30BINDING SITE FOR RESIDUE EDO A 126
17BC8SOFTWARELYS D:26 , HOH D:208 , HOH D:214 , THR E:88 , GLU E:89 , TYR E:90 , HOH E:162BINDING SITE FOR RESIDUE EDO D 123
18BC9SOFTWARECL A:122 , ASN B:30BINDING SITE FOR RESIDUE EDO B 125
19CC1SOFTWARESER A:47 , ALA A:50 , GLU A:54 , HOH A:151 , HOH A:166 , HOH A:170 , GLN C:40 , GLU C:77 , HOH C:128BINDING SITE FOR RESIDUE EDO A 127
20CC2SOFTWARETYR E:96 , GLU E:97 , ASN E:100 , ASN E:101BINDING SITE FOR RESIDUE EDO E 122
21CC3SOFTWARETYR D:25 , GLN E:32 , LYS E:33 , TYR E:90 , HOH E:153 , HOH E:162 , HOH E:173BINDING SITE FOR RESIDUE EDO E 123

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RLD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RLD)

(-) 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:114
 aligned with Q8AAW0_BACTN | Q8AAW0 from UniProtKB/TrEMBL  Length:120

    Alignment length:116
                             1                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109      
         Q8AAW0_BACTN     - -MREDMKDNVVKDKSLEFAVRIVNLYKFLVNEQKEFVMSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIK 115
               SCOP domains -d2rlda1 A:1-115 Uncharacterized protein BT0352                                                                      SCOP domains
               CATH domains 2rldA00 A:0-115 IVS-encoded domain-like                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.--hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2rld A   0 GmREDmKDNVVKDKSLEFAVRIVNLYKFLVNEQKEFVmSKQILRSGTSIGANIREAEQ--SRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIK 115
                             |   |   9        19        29       |39        49       | -|       69        79        89        99       109      
                             |   |                              37-MSE              57 60                                                       
                             1-MSE                                                                                                              
                                 5-MSE                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with Q8AAW0_BACTN | Q8AAW0 from UniProtKB/TrEMBL  Length:120

    Alignment length:112
                                    14        24        34        44        54        64        74        84        94       104       114  
         Q8AAW0_BACTN     5 MKDNVVKDKSLEFAVRIVNLYKFLVNEQKEFVMSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKT 116
               SCOP domains d2rldb_ B: Uncharacterized protein BT0352                                                                        SCOP domains
               CATH domains -2rldB00 B:6-116 IVS-encoded domain-like                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2rld B   5 mKDNVVKDKSLEFAVRIVNLYKFLVNEQKEFVmSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKT 116
                            |       14        24        34  |     44        54        64        74        84        94       104       114  
                            5-MSE                          37-MSE                                                                           


Chain C from PDB  Type:PROTEIN  Length:116
 aligned with Q8AAW0_BACTN | Q8AAW0 from UniProtKB/TrEMBL  Length:120

    Alignment length:116
                                    10        20        30        40        50        60        70        80        90       100       110      
         Q8AAW0_BACTN     1 MREDMKDNVVKDKSLEFAVRIVNLYKFLVNEQKEFVMSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKT 116
               SCOP domains d2rldc_ C: Uncharacterized protein BT0352                                                                            SCOP domains
               CATH domains -2rldC00 C:2-116 IVS-encoded domain-like                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2rld C   1 mREDmKDNVVKDKSLEFAVRIVNLYKFLVNEQKEFVmSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKT 116
                            |   |   10        20        30      | 40        50        60        70        80        90       100       110      
                            1-MSE                              37-MSE                                                                           
                                5-MSE                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:108
 aligned with Q8AAW0_BACTN | Q8AAW0 from UniProtKB/TrEMBL  Length:120

    Alignment length:108
                                    16        26        36        46        56        66        76        86        96       106        
         Q8AAW0_BACTN     7 DNVVKDKSLEFAVRIVNLYKFLVNEQKEFVMSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISII 114
               SCOP domains d2rldd_ D: Uncharacterized protein BT0352                                                                    SCOP domains
               CATH domains 2rldD00 D:7-114 IVS-encoded domain-like                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2rld D   7 DNVVKDKSLEFAVRIVNLYKFLVNEQKEFVmSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISII 114
                                    16        26        36|       46        56        66        76        86        96       106        
                                                         37-MSE                                                                         


Chain E from PDB  Type:PROTEIN  Length:110
 aligned with Q8AAW0_BACTN | Q8AAW0 from UniProtKB/TrEMBL  Length:120

    Alignment length:110
                                    17        27        37        47        57        67        77        87        97       107       117
         Q8AAW0_BACTN     8 NVVKDKSLEFAVRIVNLYKFLVNEQKEFVMSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKTT 117
               SCOP domains d2rlde_ E: Uncharacterized protein BT0352                                                                      SCOP domains
               CATH domains 2rldE00 E:8-117 IVS-encoded domain-like                                                                        CATH domains
           Pfam domains (1) Ribosomal_S23p-2rldE01 E:8-113                                                                            ---- Pfam domains (1)
           Pfam domains (2) Ribosomal_S23p-2rldE02 E:8-113                                                                            ---- Pfam domains (2)
           Pfam domains (3) Ribosomal_S23p-2rldE03 E:8-113                                                                            ---- Pfam domains (3)
           Pfam domains (4) Ribosomal_S23p-2rldE04 E:8-113                                                                            ---- Pfam domains (4)
           Pfam domains (5) Ribosomal_S23p-2rldE05 E:8-113                                                                            ---- Pfam domains (5)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2rld E   8 NVVKDKSLEFAVRIVNLYKFLVNEQKEFVmSKQILRSGTSIGANIREAEQAQSRADFINKLNIALKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKTT 117
                                    17        27        37        47        57        67        77        87        97       107       117
                                                        37-MSE
   Legend:   → Mismatch (orange background)
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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, 5)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Ribosomal_S23p] (1)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q8AAW0_BACTN | Q8AAW0)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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