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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE E.COLI STRESS PROTEIN YCIF.
 
Authors :  A. Hindupur, D. Liu, Y. Zhao, H. D. Bellamy, M. A. White, R. O. Fox
Date :  25 Apr 06  (Deposition) - 17 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Stress Proteins, Rubrerythrin, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hindupur, D. Liu, Y. Zhao, H. D. Bellamy, M. A. White, R. O. Fox
The Crystal Structure Of The E. Coli Stress Protein Ycif.
Protein Sci. V. 15 2605 2006
PubMed-ID: 17001035  |  Reference-DOI: 10.1110/PS.062307706
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YCIF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K-12 SUBSTR. DH10B
    Expression System Plasmid: P215
    Expression System Strain: DH10B
    Expression System Taxid: 316385
    Expression System Vector Type: PLASMID
    Gene: YCIF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K-12 MG1655

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2GS4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GS4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GS4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GS4)

(-) Exons   (0, 0)

(no "Exon" information available for 2GS4)

(-) 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:159
 aligned with YCIF_ECOLI | P21362 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152         
           YCIF_ECOLI     3 MKTIEDVFIHLLSDTYSAEKQLTRALAKLARATSNEKLSQAFHAHLEETHGQIERIDQVVESESNLKIKRMKCVAMEGLIEEANEVIESTEKNEVRDAALIAAAQKVEHYEIASYGTLATLAEQLGYRKAAKLLKETLEEEKATDIKLTDLAINNVNKK 161
               SCOP domains d2gs4a1 A:3-161 Hypothetical protein YciF                                                                                                                       SCOP domains
               CATH domains -2gs4A00 A:4-161  [code=1.20.1260.10, no name defined]                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gs4 A   3 mKTIEDVFIHLLSDTYSAEKQLTRALAKLARATSNEKLSQAFHAHLEETHGQIERIDQVVESESNLKIKRmKCVAmEGLIEEANEVIESTEKNEVRDAALIAAAQKVEHYEIASYGTLATLAEQLGYRKAAKLLKETLEEEKATDIKLTDLAINNVNKK 161
                            |       12        22        32        42        52        62        72|    |  82        92       102       112       122       132       142       152         
                            |                                                                    73-MSE|                                                                                   
                            3-MSE                                                                     78-MSE                                                                               


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with YCIF_ECOLI | P21362 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
           YCIF_ECOLI     4 KTIEDVFIHLLSDTYSAEKQLTRALAKLARATSNEKLSQAFHAHLEETHGQIERIDQVVESESNLKIKRMKCVAMEGLIEEANEVIESTEKNEVRDAALIAAAQKVEHYEIASYGTLATLAEQLGYRKAAKLLKETLEEEKATDIKLTDLAINN 157
               SCOP domains d2gs4b_ B: Hypothetical protein YciF                                                                                                                       SCOP domains
               CATH domains 2gs4B00 B:4-157  [code=1.20.1260.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gs4 B   4 KTIEDVFIHLLSDTYSAEKQLTRALAKLARATSNEKLSQAFHAHLEETHGQIERIDQVVESESNLKIKRmKCVAmEGLIEEANEVIESTEKNEVRDAALIAAAQKVEHYEIASYGTLATLAEQLGYRKAAKLLKETLEEEKATDIKLTDLAINN 157
                                    13        23        33        43        53        63        73    |   83        93       103       113       123       133       143       153    
                                                                                                73-MSE|                                                                               
                                                                                                     78-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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GS4)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YCIF_ECOLI | P21362)
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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