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(-) Description

Title :  CRYSTAL STRUCTURE OF AN UNCHARACTERTIZED PROTEIN FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  S. Eswaramoorthy, S. C. Almo, S. Swaminathan, New York Structural G Research Consortium (Nysgrc)
Date :  22 Mar 11  (Deposition) - 06 Apr 11  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Psi-Biology, Structural Genomics, New York Structural Genomics Research Consortium, Tim Barrel, Alanine Racemase, Ybl036C-Like Proteins, Pyridoxal 5' Phosphate, Metal Ion, Structure Genomics, Unknown Function, Nysgrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. C. Almo, S. Swaminathan
Crystal Structure Of An Uncharactertized Protein From Agrobacterium Tumefaciens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AGR_C_4983, ATU2747, PLPDE_III_YBL036C_LIKE
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4PR2Ligand/IonPRASEODYMIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
3PLP-1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4PR-1Ligand/IonPRASEODYMIUM ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4PR-1Ligand/IonPRASEODYMIUM ION
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4PR-1Ligand/IonPRASEODYMIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:5 , GLU A:9 , HOH A:247 , HOH A:332 , GLU B:204 , HOH B:282 , HOH B:321BINDING SITE FOR RESIDUE PR A 243
2AC2SOFTWAREGLU A:133 , ACT B:244 , PLP B:258 , HOH B:303 , HOH B:304 , HOH B:320BINDING SITE FOR RESIDUE PR B 243
3AC3SOFTWAREGLN A:135 , MSE B:195 , SER B:196 , GLY B:197 , ASP B:198 , PR B:243 , PLP B:258BINDING SITE FOR RESIDUE ACT B 244
4AC4SOFTWAREPRO A:134 , LYS B:36 , ILE B:81 , MSE B:195 , SER B:196 , ARG B:211 , VAL B:212 , GLY B:213 , SER B:214 , ARG B:220 , PR B:243 , ACT B:244 , HOH B:303BINDING SITE FOR RESIDUE PLP B 258

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R79)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R79)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R79)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R79)

(-) Exons   (0, 0)

(no "Exon" information available for 3R79)

(-) 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:228
 aligned with A9CHE9_AGRFC | A9CHE9 from UniProtKB/TrEMBL  Length:220

    Alignment length:228
                                                                                                                                                                                                                                                    220         
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        |-        
         A9CHE9_AGRFC     2 MEIEARLEDVRQRIADVAEKSGRKAADVALVAVSKTFDAEAIQPVIDAGQRVFGENRVQEAQGKWPALKEKTSDIELHLIGPLQSNKAADAVALFDVVESIDREKIARALSEECARQGRSLRFYVQVNTGLEPQKAGIDPRETVAFVAFCRDELKLPVEGLMCIPPAEENPGPHFALLAKLAGQCGLEKLSMGMSGDFETAVEFGATSVRVGSAIFGSR---------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhheeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhh......eee........hhhhhhhhhhhhhhhh..eee.....hhhhhhhh...eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r79 A   2 mEIEARLEDVRQRIADVAEKSGRKAADVALVAVSKTFDAEAIQPVIDAGQRVFGENRVQEAQGKWPALKEKTSDIELHLIGPLQSNKAADAVALFDVVESIDREKIARALSEECARQGRSLRFYVQVNTGLEPQKAGIDPRETVAFVAFCRDELKLPVEGLmCIPPAEENPGPHFALLAKLAGQCGLEKLSmGmSGDFETAVEFGATSVRVGSAIFGSRAENLYFQSH 229
                            |       11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 |     171       181       191 | |   201       211       221        
                            |                                                                                                                                                              163-MSE                       193-MSE                                
                            2-MSE                                                                                                                                                                                          195-MSE                              


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with A9CHE9_AGRFC | A9CHE9 from UniProtKB/TrEMBL  Length:220

    Alignment length:224
                                                                                                                                                                                                                                                   220      
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       | -    
         A9CHE9_AGRFC     3 EIEARLEDVRQRIADVAEKSGRKAADVALVAVSKTFDAEAIQPVIDAGQRVFGENRVQEAQGKWPALKEKTSDIELHLIGPLQSNKAADAVALFDVVESIDREKIARALSEECARQGRSLRFYVQVNTGLEPQKAGIDPRETVAFVAFCRDELKLPVEGLMCIPPAEENPGPHFALLAKLAGQCGLEKLSMGMSGDFETAVEFGATSVRVGSAIFGSR------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhheeeee....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh...eeeee.....--.....hhhhhhhhhhhhhhh....eeeee.....-..hhhhhhhhhhhhhhhh..eee.....hhhhhhhh...eeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r79 B   3 EIEARLEDVRQRIADVAEKSGRKAADVALVAVSKTFDAEAIQPVIDAGQRVFGENRVQEAQGKWPALKEKTSDIELHLIGPLQSNKAADAVALFDVVESIDREKIARALSEECARQGRSLRFYVQVNTGL--QKAGIDPRETVAFVAFCRDELKLPVEGLmCIPPA-ENPGPHFALLAKLAGQCGLEKLSmGmSGDFETAVEFGATSVRVGSAIFGSRAENLYF 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |    142       152       162|    | 172       182       192| |    202       212       222    
                                                                                                                                                           132  |                         163-MSE8 |                    193-MSE                             
                                                                                                                                                              135                                170                      195-MSE
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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  (0, 0)

(no "SCOP Domain" information available for 3R79)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R79)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R79)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3R79)

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  3r79
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