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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOTIDYLTRANSFERASE-LIKE PROTEIN (ZP_00538802.1) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Jan 08  (Deposition) - 12 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Zp_00538802. 1, Nucleotidyltransferase-Like Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nucleotidyltransferase-Like Protein (Zp_00538802. 1) From Exiguobacterium Sibiricum 255-15 At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOTIDYLTRANSFERASE-LIKE PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ZP_00538802.1, EXIGDRAFT_1952
    Organism Scientific: EXIGUOBACTERIUM SIBIRICUM
    Organism Taxid: 262543
    Strain: 255-15

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:51 , TRP A:52 , LYS B:276BINDING SITE FOR RESIDUE CL B 290
2AC2SOFTWARELYS A:276 , GLU C:51 , TRP C:52 , LYS C:252BINDING SITE FOR RESIDUE CL C 290
3AC3SOFTWAREGLU B:51 , TRP B:52 , LYS C:276BINDING SITE FOR RESIDUE CL C 291
4AC4SOFTWAREMSE A:239 , GLY A:256 , ASP A:260 , HOH A:365 , ASP B:35 , PHE B:37 , HIS B:56BINDING SITE FOR RESIDUE GOL A 290
5AC5SOFTWAREVAL A:253 , HOH A:388 , TRP B:52 , TRP B:77 , ASN B:83 , ARG B:85BINDING SITE FOR RESIDUE GOL B 291
6AC6SOFTWAREASP A:35 , GLN A:36 , PHE A:37 , HIS A:56 , MSE B:239 , GLY B:256 , ASP B:260 , TYR B:285 , HOH B:349 , HOH B:430BINDING SITE FOR RESIDUE GOL B 292
7AC7SOFTWAREARG B:137 , HIS B:205 , ILE B:209 , GLU B:212BINDING SITE FOR RESIDUE GOL B 293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C18)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C18)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C18)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C18)

(-) Exons   (0, 0)

(no "Exon" information available for 3C18)

(-) 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:290
 aligned with B1YK61_EXIS2 | B1YK61 from UniProtKB/TrEMBL  Length:289

    Alignment length:290
                             1                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
         B1YK61_EXIS2     - -MEQATRTIYSEYAAYPETQGIIAVEKRQPRDSLTDQFDVLLLVITRDPSVEWTVKHYRLNTLRVSLHLVHEQVLSRWLILNANRRAVHWVSEGTIIFERNDYLTDLKKQLRNFPETERCLQMSLSFAKLLRRFQDGRNLFSRGNYYDAYTHVHHALHHLARLSVLEKGAHPEVVVWEQARLDDPDVYKLYEQLLLSEETLEQRIHLALIGLEHLLQSKVLSGGKYLFEVMRERDRPWTMHELMEESRLTELKVDLGSLVDFFIRKGLIRISYQRTKGLGVELVTYEPVV 289
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c18A01 A:0-114 Beta Polymerase, domain 2                                                                          3c18A02 A:115-232 Nucleotidyltransferases  domain 2                                                                   3c18A03 A:233-289                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeeeeeee.....hhhhh...eeeeeee......eeeeeeee..eeeeeeeeehhhhhhhhhhh.hhhhhhhhhhheeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c18 A   0 GmEQATRTIYSEYAAYPETQGIIAVEKRQPRDSLTDQFDVLLLVITRDPSVEWTVKHYRLNTLRVSLHLVHEQVLSRWLILNANRRAVHWVSEGTIIFERNDYLTDLKKQLRNFPETERCLQmSLSFAKLLRRFQDGRNLFSRGNYYDAYTHVHHALHHLARLSVLEKGAHPEVVVWEQARLDDPDVYKLYEQLLLSEETLEQRIHLALIGLEHLLQSKVLSGGKYLFEVmRERDRPWTmHELmEESRLTELKVDLGSLVDFFIRKGLIRISYQRTKGLGVELVTYEPVV 289
                             |       9        19        29        39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189       199       209       219       229|      239   |   249       259       269       279       289
                             |                                                                                                                      122-MSE                                                                                                     230-MSE  239-MSE                                              
                             1-MSE                                                                                                                                                                                                                                           243-MSE                                          


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with B1YK61_EXIS2 | B1YK61 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                             1                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279         
         B1YK61_EXIS2     - -MEQATRTIYSEYAAYPETQGIIAVEKRQPRDSLTDQFDVLLLVITRDPSVEWTVKHYRLNTLRVSLHLVHEQVLSRWLILNANRRAVHWVSEGTIIFERNDYLTDLKKQLRNFPETERCLQMSLSFAKLLRRFQDGRNLFSRGNYYDAYTHVHHALHHLARLSVLEKGAHPEVVVWEQARLDDPDVYKLYEQLLLSEETLEQRIHLALIGLEHLLQSKVLSGGKYLFEVMRERDRPWTMHELMEESRLTELKVDLGSLVDFFIRKGLIRISYQRTKGLGVELVTYEPV 288
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c18B01 B:0-114 Beta Polymerase, domain 2                                                                          3c18B02 B:115-232 Nucleotidyltransferases  domain 2                                                                   3c18B03 B:233-288                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeeeeeee.....hhhhh...eeeeeee......eeeeeeee..eeeeeeeeehhhhhhhhhhh.hhhhhhhhhhheeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c18 B   0 GmEQATRTIYSEYAAYPETQGIIAVEKRQPRDSLTDQFDVLLLVITRDPSVEWTVKHYRLNTLRVSLHLVHEQVLSRWLILNANRRAVHWVSEGTIIFERNDYLTDLKKQLRNFPETERCLQmSLSFAKLLRRFQDGRNLFSRGNYYDAYTHVHHALHHLARLSVLEKGAHPEVVVWEQARLDDPDVYKLYEQLLLSEETLEQRIHLALIGLEHLLQSKVLSGGKYLFEVmRERDRPWTmHELmEESRLTELKVDLGSLVDFFIRKGLIRISYQRTKGLGVELVTYEPV 288
                             |       9        19        29        39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189       199       209       219       229|      239   |   249       259       269       279         
                             1-MSE                                                                                                                  122-MSE                                                                                                     230-MSE  239-MSE                                             
                                                                                                                                                                                                                                                                             243-MSE                                         


Chain C from PDB  Type:PROTEIN  Length:290
 aligned with B1YK61_EXIS2 | B1YK61 from UniProtKB/TrEMBL  Length:289

    Alignment length:290
                             1                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
         B1YK61_EXIS2     - -MEQATRTIYSEYAAYPETQGIIAVEKRQPRDSLTDQFDVLLLVITRDPSVEWTVKHYRLNTLRVSLHLVHEQVLSRWLILNANRRAVHWVSEGTIIFERNDYLTDLKKQLRNFPETERCLQMSLSFAKLLRRFQDGRNLFSRGNYYDAYTHVHHALHHLARLSVLEKGAHPEVVVWEQARLDDPDVYKLYEQLLLSEETLEQRIHLALIGLEHLLQSKVLSGGKYLFEVMRERDRPWTMHELMEESRLTELKVDLGSLVDFFIRKGLIRISYQRTKGLGVELVTYEPVV 289
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c18C01 C:0-114 Beta Polymerase, domain 2                                                                          3c18C02 C:115-232 Nucleotidyltransferases  domain 2                                                                   3c18C03 C:233-289                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeeeeeee.....hhhhh...eeeeeee......eeeeeeee..eeeeeeeeehhhhhhhhhh..hhhhhhhhhhheeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c18 C   0 GmEQATRTIYSEYAAYPETQGIIAVEKRQPRDSLTDQFDVLLLVITRDPSVEWTVKHYRLNTLRVSLHLVHEQVLSRWLILNANRRAVHWVSEGTIIFERNDYLTDLKKQLRNFPETERCLQmSLSFAKLLRRFQDGRNLFSRGNYYDAYTHVHHALHHLARLSVLEKGAHPEVVVWEQARLDDPDVYKLYEQLLLSEETLEQRIHLALIGLEHLLQSKVLSGGKYLFEVmRERDRPWTmHELmEESRLTELKVDLGSLVDFFIRKGLIRISYQRTKGLGVELVTYEPVV 289
                             |       9        19        29        39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189       199       209       219       229|      239   |   249       259       269       279       289
                             1-MSE                                                                                                                  122-MSE                                                                                                     230-MSE  239-MSE                                              
                                                                                                                                                                                                                                                                             243-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  (0, 0)

(no "SCOP Domain" information available for 3C18)

(-) CATH Domains  (3, 9)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C18)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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