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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN YFIH FROM SHIGELLA FLEXNERI, PFAM DUF152
 
Authors :  J. Seetharaman, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  12 Jul 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Hypothetical Protein, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, S. Swaminathan
Crystal Structure Of Conserved Hypothetical Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORF, CONSERVED HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:71 , CYS A:107 , HIS A:124 , HOH A:584BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREHIS B:71 , CYS B:107 , HIS B:124 , HOH B:509 , HOH B:528BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U05)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:29 -Pro A:30
2Asp A:32 -Ser A:33
3Pro B:29 -Pro B:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U05)

(-) Exons   (0, 0)

(no "Exon" information available for 1U05)

(-) 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:243
 aligned with Q83K13_SHIFL | Q83K13 from UniProtKB/TrEMBL  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
         Q83K13_SHIFL     1 MSKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
               SCOP domains d1u05a_ A: Hypothetical protein yfiH                                                                                                                                                                                                                SCOP domains
               CATH domains 1u05A00 A:1-243 CNF1/YfiH-like putative cysteine hydrolases                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.........eeeeee......................hhhhhhhhhhhhhhhhh...............eee............eeee.....eeeeee...eeeeeee.....eeeeeehhhhhhhhhhhhhhh....hhh.eeeee.........eehhhhhhhhhh.hhhhhh.eeee..eeeehhhhhhhhhhhhhh..eeee.............hhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u05 A   1 MSKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q83K13_SHIFL | Q83K13 from UniProtKB/TrEMBL  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
         Q83K13_SHIFL     1 MSKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
               SCOP domains d1u05b_ B: Hypothetical protein yfiH                                                                                                                                                                                                                SCOP domains
               CATH domains 1u05B00 B:1-243 CNF1/YfiH-like putative cysteine hydrolases                                                                                                                                                                                         CATH domains
           Pfam domains (1) ------------------Cu-oxidase_4-1u05B01 B:19-242                                                                                                                                                                                                   - Pfam domains (1)
           Pfam domains (2) ------------------Cu-oxidase_4-1u05B02 B:19-242                                                                                                                                                                                                   - Pfam domains (2)
         Sec.struct. author ..............eeeee.......................hhhhhhhhhhhhhhhh................eee............eeee.....eeeeee...eeeeeee.....eeeeeehhhhhhhhhhhhhhh....hhh.eeeee.........eehhhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhhhh...eeee.......................eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u05 B   1 MSKLIVPQWPLPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADCLPVLFCNRAGTEVAAVHAGWRGLCAGVLEETVSCFADKPENILAWLGPAIGPRAFEVGAEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLI 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Cu-oxidase_4] (6)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q83K13_SHIFL | Q83K13)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q83K13_SHIFL | Q83K13: 1xaf

(-) Related Entries Specified in the PDB File

1rv9
1rw0 RELATED ID: NYSGXRC-T899 RELATED DB: TARGETDB