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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE SOR OPERON REGULATOR FROM SHIGELLA FLEXNERI
 
Authors :  Y. Kim, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, W. F. And A. Joachimiak, Center For Structural Genomics Of Infectious D (Csgid)
Date :  08 Sep 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alpha-Beta-Alpha Sandwich, Center For Structural Genomics Of Infectious Diseases, Csgid, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, W. F. Anderson, A. Joachimiak
Crystal Structure Of Probable Sor Operon Regulator From Shigella Flexneri
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE SOR-OPERON REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 51-315
    Organism Scientific: SHIGELLA FLEXNERI 2A
    Organism Taxid: 198215
    Strain: 2457T

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 29)

Asymmetric Unit (2, 29)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:232 , MSE B:233 , LYS B:237 , HOH B:292 , HOH B:382BINDING SITE FOR RESIDUE ACY B 266

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EFB)

(-) 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:246
 aligned with Q83PA8_SHIFL | Q83PA8 from UniProtKB/TrEMBL  Length:315

    Alignment length:255
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
         Q83PA8_SHIFL    61 ENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDIALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDIHGAMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 315
               SCOP domains d3efba1 A:11-265 Sor-operon regulator SorC                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eeee.........hhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhhhhh..eeee.....---------...hhhhhhhhhhh...eee..eee..........hhhhh...hhhhhhh..eeeee.......hhhhhhhhh....eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efb A  11 ENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAmmGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGImQSQHFKTISAYWDNLDIALVGIGSP---------AFYGGEESDDLNARQVAGDICSRFFDIHGAmVETNmSEKTLSIEmNKLKQARYSIGIAmSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 265
                                    20        30        40   ||   50        60        70        80        90       100       110       120       130       140       150       160    |    -    |  180       190       200    |  210       220       230  |    240       250       260     
                                                            44-MSE                                                                                         140-MSE                  165       175                           205-MSE|      219-MSE       233-MSE                            
                                                             45-MSE                                                                                                                                                              210-MSE                                                   


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with Q83PA8_SHIFL | Q83PA8 from UniProtKB/TrEMBL  Length:315

    Alignment length:255
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310     
         Q83PA8_SHIFL    61 ENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDIALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDIHGAMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 315
               SCOP domains d3efbb_ B: automated m    atches                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeee.----hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eeee.........hhhhhhhhhhhhhhhhhh.ee..........hhhhhhhhhhhhhhhhhhhhhh...eeee.....------hhhhhh----------....eee..eee..........hhhhh...hhhhhhh..eeeee.....hhhhhhhhhhh....eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efb B  11 ENLWLEQQLKQKFGLKDVVVVS----DEETQLAmmGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGImQSQHFKTISAYWDNLDIALVGIGSP------NWHAFY----------RQVAGDICSRFFDIHGAmVETNmSEKTLSIEmNKLKQARYSIGIAmSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 265
                                    20        30 |    | 40   ||   50        60        70        80        90       100       110       120       130       140       150       160    |    - |    |  -       190       200    |  210       220       230  |    240       250       260     
                                                32   37     44-MSE                                                                                         140-MSE                  165    172  177        188              205-MSE|      219-MSE       233-MSE                            
                                                             45-MSE                                                                                                                                                              210-MSE                                                   


Chain C from PDB  Type:PROTEIN  Length:233
 aligned with Q83PA8_SHIFL | Q83PA8 from UniProtKB/TrEMBL  Length:315

    Alignment length:254
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    
         Q83PA8_SHIFL    61 ENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDIALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDIHGAMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLL 314
               SCOP domains d3efbc_ C: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhh.........eeee.........hhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhhhh...eeee.....---------------------...eeee....eee.........hhhhh...hhhhhhh..eeeee.....hhhhhhhhhhh....eeeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efb C  11 ENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAmmGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGImQSQHFKTISAYWDNLDIALVGIGSP---------------------ARQVAGDICSRFFDIHGAmVETNmSEKTLSIEmNKLKQARYSIGIAmSEEKYSGIIGALRGKYINCLVTNSSTAELLL 264
                                    20        30        40   ||   50        60        70        80        90       100       110       120       130       140       150       160    |    -         -      |190       200    |  210       220       230  |    240       250       260    
                                                            44-MSE                                                                                         140-MSE                  165                   187               205-MSE|      219-MSE       233-MSE                           
                                                             45-MSE                                                                                                                                                              210-MSE                                                  


Chain D from PDB  Type:PROTEIN  Length:248
 aligned with Q83PA8_SHIFL | Q83PA8 from UniProtKB/TrEMBL  Length:315

    Alignment length:256
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309      
         Q83PA8_SHIFL    60 NENLWLEQQLKQKFGLKDVVVVSGNDEDEETQLAMMGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGIMQSQHFKTISAYWDNLDIALVGIGSPAIRDGANWHAFYGGEESDDLNARQVAGDICSRFFDIHGAMVETNMSEKTLSIEMNKLKQARYSIGIAMSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 315
               SCOP domains d3efbd_ D: automated mat  ches                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeeee..--.hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eeee.........hhhhhhhhhhhhhhhhh..ee..........hhhhhhhhh.hhhhhhhhhhhhh..eeeee....------hhhhhhhhhhhhhhhhh...eee..eee..................hhhhhh...eeeee.....hhhhhhhhhhh....eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3efb D  10 NENLWLEQQLKQKFGLKDVVVVSG--EDEETQLAmmGLHGAQLLDRLLEPGDIVGFSWGRAVSALVENLPQAGQSRQLICVPIIGGPSGKLESRYHVNTLTYSAAAKLKGESHLADFPALLDNPLIRNGImQSQHFKTISAYWDNLDIALVGIGSP------NWHAFYGGEESDDLNARQVAGDICSRFFDIHGAmVETNmSEKTLSIEmNKLKQARYSIGIAmSEEKYSGIIGALRGKYINCLVTNSSTAELLLK 265
                                    19        29   |  | 39    ||  49        59        69        79        89        99       109       119       129       139|      149       159     |   -  |    179       189       199     | 209|      219       229   |   239       249       259      
                                                  33 36      44-MSE                                                                                         140-MSE                  165    172                              205-MSE|      219-MSE       233-MSE                            
                                                              45-MSE                                                                                                                                                              210-MSE
   Legend:   → Mismatch (orange background)
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    → 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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q83PA8_SHIFL | Q83PA8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.

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