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(-) Description

Title :  STRUCTURE OF PAG5_736 FROM P. AEROPHILUM WITH THREE DISULPHIDE BONDS
 
Authors :  M. Beeby, C. Ryttersgaard, D. R. Boutz, L. J. Perry, T. O. Yeates
Date :  21 Nov 03  (Deposition) - 18 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, (Beta-Alpha-Beta)X2, Beta-Loop-Beta-Beta, Cxxc Motif, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Beeby, C. Ryttersgaard, D. R. Boutz, L. J. Perry, T. O. Yeates
The Genomics Of Disulfide Bonding And Protein Stabilization In Thermophiles.
Plos Biol. V. 3 E309 2005
PubMed-ID: 16111437  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0030309

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PAG5_736
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3P6G1Ligand/IonHEXAETHYLENE GLYCOL
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3P6G-1Ligand/IonHEXAETHYLENE GLYCOL
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3P6G1Ligand/IonHEXAETHYLENE GLYCOL
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:23 , TYR B:27 , GLU B:72 , VAL B:73 , HOH B:209 , HOH B:231BINDING SITE FOR RESIDUE ACT B 201
2AC2SOFTWAREHIS A:58 , LYS A:62 , HOH A:207 , HOH A:225 , SER B:76 , LYS B:77 , HOH B:243BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREHIS A:74 , ASN A:75 , SER A:76BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREHIS A:58 , ASN B:75 , HOH B:214 , HOH B:248BINDING SITE FOR RESIDUE CL B 204
5AC5SOFTWARECYS A:24 , TYR A:27 , TYR A:28 , TYR B:27 , LYS B:35 , TYR B:43 , VAL B:91 , PG4 B:206BINDING SITE FOR RESIDUE P6G B 205
6AC6SOFTWAREASP B:20 , ASP B:23 , TYR B:27 , P6G B:205BINDING SITE FOR RESIDUE PG4 B 206

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:22 -A:34
2A:24 -A:54
3A:80 -A:83
4B:22 -B:34
5B:24 -B:54
6B:80 -B:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RKI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RKI)

(-) Exons   (0, 0)

(no "Exon" information available for 1RKI)

(-) 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:101
 aligned with Q8ZYK2_PYRAE | Q8ZYK2 from UniProtKB/TrEMBL  Length:98

    Alignment length:101
                                                                                                                            98   
                                    10        20        30        40        50        60        70        80        90       | - 
         Q8ZYK2_PYRAE     1 MKKHIIIKTIPKKEEIISRDLCDCIYYYDNSVICKPIGPSKVYVSTSLENLEKCLQLHYFKKLVKNIEIFDEVHNSKPNCDKCLIVEIGGVYFVRRVN---   -
               SCOP domains d1rkia1 A:1-98 Hypothetical protein PAE0736                                                       --- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhh......eeeeee..eeeeeehhhhhhhhhhhhhhhh.eeeeeee.eee........eeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1rki A   1 MKKHIIIKTIPKKEEIISRDLCDCIYYYDNSVICKPIGPSKVYVSTSLENLEKCLQLHYFKKLVKNIEIFDEVHNSKPNCDKCLIVEIGGVYFVRRVNGVP 101
                                    10        20        30        40        50        60        70        80        90       100 


Chain B from PDB  Type:PROTEIN  Length:97
 aligned with Q8ZYK2_PYRAE | Q8ZYK2 from UniProtKB/TrEMBL  Length:98

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
         Q8ZYK2_PYRAE     1 MKKHIIIKTIPKKEEIISRDLCDCIYYYDNSVICKPIGPSKVYVSTSLENLEKCLQLHYFKKLVKNIEIFDEVHNSKPNCDKCLIVEIGGVYFVRRV  97
               SCOP domains d1rkib_ B: Hypothetical protein PAE0736                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---DUF3195-1rkiB01 B:4-92                                                                   ----- Pfam domains (1)
           Pfam domains (2) ---DUF3195-1rkiB02 B:4-92                                                                   ----- Pfam domains (2)
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhh...eeeee.eee.........eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1rki B   1 MKKHIIIKTIPKKEEIISRDLCDCIYYYDNSVICKPIGPSKVYVSTSLENLEKCLQLHYFKKLVKNIEIFDEVHNSKPNCDKCLIVEIGGVYFVRRV  97
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
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  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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RKI)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF3195] (1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1RKI)

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