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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN YLBA FROM E. COLI, PFAM DUF861
 
Authors :  A. A. Fedorov, E. V. Fedorov, R. Thirumuruhan, U. A. Ramagopal, S. C. Alm S. K. Burley, New York Sgx Research Center For Structural Geno (Nysgxrc)
Date :  03 Nov 03  (Deposition) - 18 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (4x)
Keywords :  Structural Genomics, Nysgxrc, Sgx Clone Name 3174C1Tct3B1, Target T1521, Hypothetical Protein Ylba From E. Coli, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, R. Thirumuruhan, U. A. Ramagopal, S. C. Almo
Crystal Structure Of Ylba, Hypothetical Protein From E. Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YLBA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YLBA, GLXB6, B0515
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1RC6)

(-) Sites  (0, 0)

(no "Site" information available for 1RC6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RC6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RC6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RC6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RC6)

(-) Exons   (0, 0)

(no "Exon" information available for 1RC6)

(-) 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:242
 aligned with ALLE_ECOLI | P75713 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:253
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258   
          ALLE_ECOLI      9 GYREDLLANRAIVKHGNFALLTPDGLVKNIIPGFENCDATILSTPKLGASFVDYLVTLHQNGGNQQGFGGEGIETFLYVISGNITAKAEGKTFALSEGGYLYCPPGSLMTFVNAQAEDSQIFLYKRRYVPVEGYAPWLVSGNASELERIHYEGMDDVILLDFLPKELGFDMNMHILSFAPGASHGYIETHVQEHGAYILSGQGVYNLDNNWIPVKKGDYIFMGAYSLQAGYGVGRGEAFSYIYSKDCNRDVEI  261
               SCOP domains d1rc6a_ A: Hypothetical protein YlbA                                                                                                                                                                                                                          SCOP domains
               CATH domains 1rc6A00 A:1009-1261 Jelly Rolls                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....ee....eeeehhhhh.......eeeeeeee..hhhhh...eeeeeeeeeeeee........eeeeeeeee.eeeeee..eeeeee..eeeee......eeee.....eeeeeeeee...........eeee.hhh...-------.eeee.........eeeeeeee.......eeeee...eeeeeee.eeeee....eeeee...eeee...eeeeeee.----.eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rc6 A 1009 GYREDLLANRAIVKHGNFALLTPDGLVKNIIPGFENCDATILSTPKLGASFVDYLVTLHQNGGNQQGFGGEGIETFLYVISGNITAKAEGKTFALSEGGYLYCPPGSLMTFVNAQAEDSQIFLYKRRYVPVEGYAPWLVSGNASELERI-------VILLDFLPKELGFDMNMHILSFAPGASHGYIETHVQEHGAYILSGQGVYNLDNNWIPVKKGDYIFMGAYSLQAGYGV----AFSYIYSKDCNRDVEI 1261
                                  1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148        |-      1168      1178      1188      1198      1208      1218      1228      1238  |   1248      1258   
                                                                                                                                                                             1157    1165                                                                        1241 1246               


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with ALLE_ECOLI | P75713 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:253
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258   
          ALLE_ECOLI      9 GYREDLLANRAIVKHGNFALLTPDGLVKNIIPGFENCDATILSTPKLGASFVDYLVTLHQNGGNQQGFGGEGIETFLYVISGNITAKAEGKTFALSEGGYLYCPPGSLMTFVNAQAEDSQIFLYKRRYVPVEGYAPWLVSGNASELERIHYEGMDDVILLDFLPKELGFDMNMHILSFAPGASHGYIETHVQEHGAYILSGQGVYNLDNNWIPVKKGDYIFMGAYSLQAGYGVGRGEAFSYIYSKDCNRDVEI  261
               SCOP domains d1rc6b_ B: Hypothetical protein YlbA                                                                                                                                                                                                                          SCOP domains
               CATH domains 1rc6B00 B:1009-1261 Jelly Rolls                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....ee....eeeehhhhh.......eeeeeeee..hhhhh...eeeeeeeeeeeee........eeeeeeeee.eeeeee..eeeeee..eeeee.....eeeee.....eeeeeeeee...........eeee.hhh...-------.eeee.........eeeeeee........eeeee...eeeeeee.eeeee....eeeee...eeee...eeeeeee.----..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rc6 B 1009 GYREDLLANRAIVKHGNFALLTPDGLVKNIIPGFENCDATILSTPKLGASFVDYLVTLHQNGGNQQGFGGEGIETFLYVISGNITAKAEGKTFALSEGGYLYCPPGSLMTFVNAQAEDSQIFLYKRRYVPVEGYAPWLVSGNASELERI-------VILLDFLPKELGFDMNMHILSFAPGASHGYIETHVQEHGAYILSGQGVYNLDNNWIPVKKGDYIFMGAYSLQAGYGV----AFSYIYSKDCNRDVEI 1261
                                  1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148        |-      1168      1178      1188      1198      1208      1218      1228      1238  |   1248      1258   
                                                                                                                                                                             1157    1165                                                                        1241 1246
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RC6)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ALLE_ECOLI | P75713)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0071522    ureidoglycine aminohydrolase activity    Catalysis of the reaction: ureidoglycine + H2O = S-ureidoglycolate + NH3.
biological process
    GO:0006144    purine nucleobase metabolic process    The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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