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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN OF NTRX FROM BRUCELLA ABORTUS
 
Authors :  S. Klinke, I. Fernandez, M. C. Carrica, L. H. Otero, F. A. Goldbaum
Date :  18 Nov 14  (Deposition) - 08 Jul 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Signaling Protein, Brucellosis, Two-Component System, Response Regulator, Rec Domain, Microaerobisis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Fernandez, L. H. Otero, S. Klinke, M. C. Carrica, F. A. Goldbaum
Snapshots Of Conformational Changes Shed Light Into The Ntrx Receiver Domain Signal Transduction Mechanism
J. Mol. Biol. V. 427 3258 2015
PubMed-ID: 26113057  |  Reference-DOI: 10.1016/J.JMB.2015.06.010

(-) Compounds

Molecule 1 - BACTERIAL REGULATORY, FIS FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector Type: PLASMID
    Fragment: RECEIVER DOMAIN, RESIDUES 1-126
    Organism Scientific: BRUCELLA ABORTUS
    Organism Taxid: 235
    Other Details: THE GENE SEQUENCE ENCODING THE RECEIVER DOMAIN C-TERMINAL REGION (RESIDUES 127-136) WAS OMITTED FROM THE FINAL CONSTRUCT DUE TO POTENTIAL CLASHES INTO THE CRYSTAL PACKING
    Strain: BRUCELLA MELITENSIS BIOVAR ABORTUS 2308
    Synonym: NTRX

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1IMD3Ligand/IonIMIDAZOLE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1IMD-1Ligand/IonIMIDAZOLE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:101 , PHE A:102 , ARG A:111 , ILE B:88BINDING SITE FOR RESIDUE IMD A1124
2AC2SOFTWAREILE A:88 , GLU A:89 , ASP B:101 , PHE B:102 , ARG B:111 , HOH B:2006BINDING SITE FOR RESIDUE IMD B1124
3AC3SOFTWAREASP A:10 , GLU A:11 , ASP A:53 , TRP A:55 , HOH A:2004BINDING SITE FOR RESIDUE IMD A1125

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D6X)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:105 -Pro A:106
2Lys B:105 -Pro B:106
3Lys C:105 -Pro C:106
4Lys D:105 -Pro D:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D6X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D6X)

(-) Exons   (0, 0)

(no "Exon" information available for 4D6X)

(-) 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:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4d6x A   4 DILVVDDEVDIRDLVAGILSDEGHETRTAFDADSALAAINDRAPRLVFLDIWLQGSRLDGLALLDEIKKQHPELPVVMISGHGNIETAVSAIRRGAYDFIEKPFKADRLILVAERALETS 123
                                    13        23        33        43        53        63        73        83        93       103       113       123


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4d6x B   4 DILVVDDEVDIRDLVAGILSDEGHETRTAFDADSALAAINDRAPRLVFLDIWLQGSRLDGLALLDEIKKQHPELPVVMISGHGNIETAVSAIRRGAYDFIEKPFKADRLILVAERALETS 123
                                    13        23        33        43        53        63        73        83        93       103       113       123


Chain C from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4d6x C   4 DILVVDDEVDIRDLVAGILSDEGHETRTAFDADSALAAINDRAPRLVFLDIWLQGSRLDGLALLDEIKKQHPELPVVMISGHGNIETAVSAIRRGAYDFIEKPFKADRLILVAERALET 122
                                    13        23        33        43        53        63        73        83        93       103       113         


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4d6x D   4 DILVVDDEVDIRDLVAGILSDEGHETRTAFDADSALAAINDRAPRLVFLDIWLQGSRLDGLALLDEIKKQHPELPVVMISGHGNIETAVSAIRRGAYDFIEKPFKADRLILVAERALET 122
                                    13        23        33        43        53        63        73        83        93       103       113
   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  (0, 0)

(no "SCOP Domain" information available for 4D6X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D6X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D6X)

(-) Gene Ontology  (9, 9)

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 Related Entries

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        Q2YPW6_BRUA2 | Q2YPW6: 4d6y

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