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(-) Description

Title :  YCFI, A PUTATIVE STRUCTURAL PROTEIN FROM RHODOPSEUDOMONAS PALUSTRIS.
 
Authors :  J. Osipiuk, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  09 May 06  (Deposition) - 13 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Apc6105, Iron-Binding, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Ycfi Protein, A Putative Structural Protein From Rhodopseudomonas Palustris.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YCFI, PUTATIVE STRUCTURAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RPA3308
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 258594
    Strain: CGA009

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric/Biological Unit (5, 18)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FE5Ligand/IonFE (III) ION
4NA1Ligand/IonSODIUM ION
5ZN6Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:52 , GLU A:114 , GLU A:117 , GLU A:147 , ZN A:407 , ZN A:409 , HOH A:534 , HOH A:585BINDING SITE FOR RESIDUE FE A 401
02AC2SOFTWAREASP A:21 , CYS A:79 , TYR A:116 , GLU B:88BINDING SITE FOR RESIDUE FE A 402
03AC3SOFTWAREGLU A:88 , ASP B:21 , CYS B:79 , TYR B:116BINDING SITE FOR RESIDUE FE A 403
04AC4SOFTWAREGLU B:26 , GLN B:59 , GLU B:117 , GLU B:147 , FE B:405 , HOH B:428BINDING SITE FOR RESIDUE FE B 404
05AC5SOFTWAREHIS B:52 , GLU B:114 , GLU B:117 , GLU B:147 , FE B:404 , HOH B:428 , HOH B:567BINDING SITE FOR RESIDUE FE B 405
06AC6SOFTWAREHIS A:17 , GLU B:95 , HOH B:434 , HOH B:493 , HOH B:550BINDING SITE FOR RESIDUE ZN B 406
07AC7SOFTWAREGLU A:26 , GLN A:59 , GLU A:117 , GLU A:147 , FE A:401 , HOH A:534BINDING SITE FOR RESIDUE ZN A 407
08AC8SOFTWAREASP A:135 , HOH A:498 , GLU B:12 , HIS B:133BINDING SITE FOR RESIDUE ZN B 408
09AC9SOFTWAREHIS A:52 , GLU A:114 , FE A:401 , HOH A:459 , HOH A:585BINDING SITE FOR RESIDUE ZN A 409
10BC1SOFTWAREGLU A:95 , HOH A:419 , HOH A:568 , HIS B:17BINDING SITE FOR RESIDUE ZN A 410
11BC2SOFTWAREGLU A:95 , HOH A:554 , HOH A:568 , HIS B:17BINDING SITE FOR RESIDUE ZN A 418
12BC3SOFTWAREASP A:7 , HOH A:547 , ASP B:44 , HOH B:482 , HOH B:526BINDING SITE FOR RESIDUE NA A 411
13BC4SOFTWAREILE A:118 , HIS B:115 , ASN B:151 , ASN B:155 , HOH B:420 , HOH B:511 , HOH B:552BINDING SITE FOR RESIDUE ACT B 414
14BC5SOFTWAREILE B:29 , LEU B:33 , HIS B:52 , ALA B:110 , VAL B:113 , GLU B:114 , HOH B:567BINDING SITE FOR RESIDUE ACT B 415
15BC6SOFTWAREARG A:62 , HOH A:592 , GLN B:72 , LYS B:73 , HOH B:454BINDING SITE FOR RESIDUE ACT A 416
16BC7SOFTWAREGLN A:111 , HIS A:115 , ASN A:151 , ASN A:155 , HOH A:472 , HOH A:556 , HOH A:564 , HOH A:595 , HOH A:596BINDING SITE FOR RESIDUE ACT A 417
17BC8SOFTWARELYS A:87 , HOH A:444 , ARG B:138 , PHE B:139 , THR B:142 , HOH B:522BINDING SITE FOR RESIDUE EDO B 412
18BC9SOFTWAREHOH A:457 , ARG B:120 , TRP B:127 , HOH B:418 , HOH B:480 , HOH B:516 , HOH B:551BINDING SITE FOR RESIDUE EDO B 413

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GYQ)

(-) 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:162
 aligned with Q6N4M9_RHOPA | Q6N4M9 from UniProtKB/TrEMBL  Length:169

    Alignment length:169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160         
         Q6N4M9_RHOPA     1 MGFFSRDIQTMEDLLLHGLRDIYYAEQQITKALPKMIEQATNRDLSQGLTSHLEETQKQIERLDQVFKKLGQKPSGVNCPAIDGLIKEADETAGEIADKTVLDAAIVANAQAVEHYEIARYGTLIAWAEELGHDDIVRFLTTNLNEEKAANTKLNTVALRKGVNRKAAS 169
               SCOP domains d2gyqa1 A:1-160 Hypothetical ptotein RPA3308                                                                                                                    --------- SCOP domains
               CATH domains 2gyqA00 A:1-169  [code=1.20.1260.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...-------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gyq A   1 MGFFSRDIQTMEDLLLHGLRDIYYAEQQITKALPKMIEQATNRDLSQGLTSHLEETQKQIERLDQVFKKLGQKPSGVNCPAIDGLIKEADETAGEIADKTVLDAAIVANAQAVEHYEIARYGTLIAWAEELGHDDIVRFLTTNLNEEKAANTKLNTVALR-------AS 169
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       | 
                                                                                                                                                                                         160     168 


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q6N4M9_RHOPA | Q6N4M9 from UniProtKB/TrEMBL  Length:169

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
         Q6N4M9_RHOPA     3 FFSRDIQTMEDLLLHGLRDIYYAEQQITKALPKMIEQATNRDLSQGLTSHLEETQKQIERLDQVFKKLGQKPSGVNCPAIDGLIKEADETAGEIADKTVLDAAIVANAQAVEHYEIARYGTLIAWAEELGHDDIVRFLTTNLNEEKAANTKLNTVAL 159
               SCOP domains d2gyqb_ B: Hypothetical ptotein RPA3308                                                                                                                       SCOP domains
               CATH domains 2gyqB00 B:3-159  [code=1.20.1260.10, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gyq B   3 FFSRDIQTMEDLLLHGLRDIYYAEQQITKALPKMIEQATNRDLSQGLTSHLEETQKQIERLDQVFKKLGQKPSGVNCPAIDGLIKEADETAGEIADKTVLDAAIVANAQAVEHYEIARYGTLIAWAEELGHDDIVRFLTTNLNEEKAANTKLNTVAL 159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6N4M9_RHOPA | Q6N4M9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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