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(-) Description

Title :  CRYSTAL STRUCTURE OF NOLR FROM SINORHIZOBIUM FREDII
 
Authors :  S. G. Lee, H. B. Krishnan, J. M. Jez
Date :  28 Jan 14  (Deposition) - 16 Apr 14  (Release) - 04 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Helix-Turn-Helix, Transcription Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Lee, H. B. Krishnan, J. M. Jez
Structural Basis For Regulation Of Rhizobial Nodulation And Symbiosis Gene Expression By The Regulatory Protein Nolr.
Proc. Natl. Acad. Sci. Usa V. 111 6509 2014
PubMed-ID: 24733893  |  Reference-DOI: 10.1073/PNAS.1402243111

(-) Compounds

Molecule 1 - NOLR
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NOLR
    Organism Scientific: SINORHIZOBIUM FREDII
    Organism Taxid: 380

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1PO414Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:13 , GLU A:17 , PRO B:29 , LYS B:30BINDING SITE FOR RESIDUE PO4 B 201
02AC2SOFTWAREPRO A:29 , LYS A:30 , HIS B:13 , GLU B:17BINDING SITE FOR RESIDUE PO4 B 202
03AC3SOFTWAREHIS C:13 , GLU C:17 , PRO D:29 , LYS D:30BINDING SITE FOR RESIDUE PO4 C 201
04AC4SOFTWAREASN C:28 , ARG C:31 , LYS C:65BINDING SITE FOR RESIDUE PO4 C 202
05AC5SOFTWAREARG D:31 , LYS D:65BINDING SITE FOR RESIDUE PO4 D 201
06AC6SOFTWARELYS C:30 , LEU C:33 , HIS D:13 , GLU D:17BINDING SITE FOR RESIDUE PO4 D 202
07AC7SOFTWAREHIS E:13 , GLU E:17 , PRO F:29 , LYS F:30BINDING SITE FOR RESIDUE PO4 E 201
08AC8SOFTWAREARG E:31 , LYS E:65BINDING SITE FOR RESIDUE PO4 E 202
09AC9SOFTWAREASN F:28 , ARG F:31 , LYS F:65 , HOH F:307BINDING SITE FOR RESIDUE PO4 F 201
10BC1SOFTWAREPRO E:29 , LYS E:30 , HIS F:13 , GLU F:17BINDING SITE FOR RESIDUE PO4 F 202
11BC2SOFTWAREHIS G:13 , GLU G:17 , PRO H:29 , LYS H:30BINDING SITE FOR RESIDUE PO4 G 201
12BC3SOFTWAREARG G:31 , LYS G:65BINDING SITE FOR RESIDUE PO4 G 202
13BC4SOFTWAREARG H:31 , LYS H:65 , HOH H:316BINDING SITE FOR RESIDUE PO4 H 201
14BC5SOFTWAREPRO G:29 , LYS G:30 , HIS H:13 , GLU H:17BINDING SITE FOR RESIDUE PO4 H 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val B:39 -Lys B:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OMZ)

(-) 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:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4omz A   6 QPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYGA 103
                                    15        25        35        45        55        65        75        85        95        


Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4omz B   5 MQPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYG 102
                                    14        24        34        44        54        64        74        84        94        


Chain C from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4omz C   5 MQPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYGAA 104
                                    14        24        34        44        54        64        74        84        94       104


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4omz D   5 MQPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYG 102
                                    14        24        34        44        54        64        74        84        94        


Chain E from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4omz E   5 MQPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYG 102
                                    14        24        34        44        54        64        74        84        94        


Chain F from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4omz F   6 QPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYGA 103
                                    15        25        35        45        55        65        75        85        95        


Chain G from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4omz G   5 MQPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYG 102
                                    14        24        34        44        54        64        74        84        94        


Chain H from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh...eeeee..eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4omz H   6 QPLSPEKHEEAEIAAGFLSAMANPKRLLILDSLVKEEMAVGALANKVGLSQSALSQHLSKLRAQNLVSTRRDAQTIYYSSSSDSVMKILGALSEIYG 102
                                    15        25        35        45        55        65        75        85        95
   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 4OMZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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