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(-) Description

Title :  CRYSTAL STRUCTURE OF A CONSERVED HYPOTHETICAL PROTEIN FROM CHLOROBIUM TEPIDUM
 
Authors :  J. S. Kim, D. H. Shin, R. Kim, S. H. Kim, Berkeley Structural Genomics (Bsgc)
Date :  07 May 04  (Deposition) - 07 Dec 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  A Winged Helix-Turn-Helix, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Kim, D. H. Shin, R. Pufan, C. Huang, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Scpb From Chlorobium Tepidum, A Protei Involved In Chromosome Partitioning.
Proteins V. 62 322 2006
PubMed-ID: 16294331  |  Reference-DOI: 10.1002/PROT.20751

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PB3.1371B
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector: PET21D
    Expression System Vector Type: PLASMID
    Organism Scientific: CHLOROBIUM TEPIDUM TLS
    Organism Taxid: 194439

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 21)

Asymmetric Unit (1, 21)
No.NameCountTypeFull Name
1NO321Ligand/IonNITRATE ION
Biological Unit 1 (1, 21)
No.NameCountTypeFull Name
1NO321Ligand/IonNITRATE ION
Biological Unit 2 (1, 42)
No.NameCountTypeFull Name
1NO342Ligand/IonNITRATE ION
Biological Unit 3 (1, 11)
No.NameCountTypeFull Name
1NO311Ligand/IonNITRATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:104 , GLN A:107 , THR A:152 , PHE A:156 , GLN B:89 , SER B:93BINDING SITE FOR RESIDUE NO3 B 401
02AC2SOFTWAREGLN A:26 , LYS A:111 , ASP A:123 , TYR A:124 , SER A:125 , ILE A:126 , ASP A:127 , NO3 A:421BINDING SITE FOR RESIDUE NO3 A 402
03AC3SOFTWARESER A:19 , GLU A:20 , GLU A:21 , GLU A:154 , HOH A:431BINDING SITE FOR RESIDUE NO3 A 403
04AC4SOFTWAREARG A:91 , ARG A:94 , SER A:95BINDING SITE FOR RESIDUE NO3 A 404
05AC5SOFTWAREGLN A:82 , PRO A:86 , VAL A:87 , GLU B:3BINDING SITE FOR RESIDUE NO3 A 405
06AC6SOFTWAREPRO A:38 , THR A:110 , LYS A:111 , GLY A:112 , PRO A:147 , HOH A:450BINDING SITE FOR RESIDUE NO3 A 406
07AC7SOFTWAREGLN A:42 , VAL A:45 , ILE A:61 , HIS A:62 , ALA A:63 , NO3 A:420 , HOH A:435BINDING SITE FOR RESIDUE NO3 A 407
08AC8SOFTWAREGLN A:89 , ARG A:90 , SER A:93 , ALA B:104 , GLN B:107 , THR B:152 , PHE B:156BINDING SITE FOR RESIDUE NO3 A 408
09AC9SOFTWAREGLN B:26 , LYS B:111 , ASP B:123 , TYR B:124 , SER B:125 , ILE B:126 , ASP B:127BINDING SITE FOR RESIDUE NO3 B 409
10BC1SOFTWARESER B:19 , GLU B:20 , GLU B:21 , GLU B:154 , HOH B:428BINDING SITE FOR RESIDUE NO3 B 410
11BC2SOFTWAREARG B:91 , ARG B:94 , SER B:95 , GLU B:98 , ARG B:118BINDING SITE FOR RESIDUE NO3 B 411
12BC3SOFTWAREPRO B:38 , THR B:110 , LYS B:111 , GLY B:112 , PRO B:147 , HOH B:445BINDING SITE FOR RESIDUE NO3 B 412
13BC4SOFTWAREPRO B:86 , VAL B:87BINDING SITE FOR RESIDUE NO3 B 413
14BC5SOFTWAREGLN B:42 , VAL B:45 , ILE B:61 , HIS B:62 , ALA B:63 , TYR B:68 , NO3 B:419 , HOH B:431BINDING SITE FOR RESIDUE NO3 B 414
15BC6SOFTWAREGLU A:40BINDING SITE FOR RESIDUE NO3 A 416
16BC7SOFTWAREGLU A:98 , HOH A:448 , TRP B:105 , HIS B:106 , ILE B:117BINDING SITE FOR RESIDUE NO3 B 417
17BC8SOFTWAREARG A:140 , HIS B:62 , ALA B:63 , ILE B:64 , NO3 B:414BINDING SITE FOR RESIDUE NO3 B 419
18BC9SOFTWAREHIS A:62 , ALA A:63 , ILE A:64 , NO3 A:407 , ARG B:140BINDING SITE FOR RESIDUE NO3 A 420
19CC1SOFTWAREGLN A:26 , LYS A:111 , NO3 A:402BINDING SITE FOR RESIDUE NO3 A 421
20CC2SOFTWAREALA A:77 , ARG A:81 , GLN B:107 , PRO B:108 , ARG B:138BINDING SITE FOR RESIDUE NO3 B 422

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6S)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gln A:107 -Pro A:108
2Ser A:121 -Pro A:122
3Gln B:107 -Pro B:108
4Ser B:121 -Pro B:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6S)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6S)

(-) 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:162
 aligned with Q8KF54_CHLTE | Q8KF54 from UniProtKB/TrEMBL  Length:209

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8KF54_CHLTE     1 MQEQRQQLLRSLEALIFSSEEPVNLQTLSQITAHKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEPEFADLVRQLLAPVIQRRLSRSMLEVLAVVAWHQPVTKGEIQQIRGASPDYSIDRLLARGLIEVRGRADSPGRPLQYGTTEVFLDLFHL 162
               SCOP domains d1t6sa1 A:1-85 Segregation and condensation protein B, ScpB                          d1t6sa2 A:86-162 Segregation and condensation protein B, ScpB                 SCOP domains
               CATH domains 1t6sA01 A:1-86 'winged helix' repressor DNA binding domain                            1t6sA02 A:87-162 'winged helix' repressor DNA binding domain                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh....hhhhhhhhh..eeeeee.......eeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6s A   1 MQEQRQQLLRSLEALIFSSEEPVNLQTLSQITAHKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEPEFADLVRQLLAPVIQRRLSRSMLEVLAVVAWHQPVTKGEIQQIRGASPDYSIDRLLARGLIEVRGRADSPGRPLQYGTTEVFLDLFHL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with Q8KF54_CHLTE | Q8KF54 from UniProtKB/TrEMBL  Length:209

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q8KF54_CHLTE     1 MQEQRQQLLRSLEALIFSSEEPVNLQTLSQITAHKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEPEFADLVRQLLAPVIQRRLSRSMLEVLAVVAWHQPVTKGEIQQIRGASPDYSIDRLLARGLIEVRGRADSPGRPLQYGTTEVFLDLFHL 162
               SCOP domains d1t6sb1 B:1-85 Segregation and condensation protein B, ScpB                          d1t6sb2 B:86-162 Segregation and condensation protein B, ScpB                 SCOP domains
               CATH domains 1t6sB01 B:1-85 'winged helix' repressor DNA binding domain                           1t6sB02 B:86-162 'winged helix' repressor DNA binding domain                  CATH domains
           Pfam domains (1) ---------DUF387-1t6sB01 B:10-162                                                                                                                                   Pfam domains (1)
           Pfam domains (2) ---------DUF387-1t6sB02 B:10-162                                                                                                                                   Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh....hhhhhhhhh..eeeeee.......eeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6s B   1 MQEQRQQLLRSLEALIFSSEEPVNLQTLSQITAHKFTPSELQEAVDELNRDYEATGRTFRIHAIAGGYRFLTEPEFADLVRQLLAPVIQRRLSRSMLEVLAVVAWHQPVTKGEIQQIRGASPDYSIDRLLARGLIEVRGRADSPGRPLQYGTTEVFLDLFHL 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8KF54_CHLTE | Q8KF54)
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0051304    chromosome separation    The cell cycle process in which paired chromosomes are detached from each other. Chromosome separation begins with the release of cohesin complexes from chromosomes; in budding yeast, this includes the cleavage of cohesin complexes along the chromosome arms, followed by the separation of the centromeric regions. Chromosome separation also includes formation of chromatid axes mediated by condensins, and ends with the disentangling of inter-sister catenation catalyzed by topoisomerase II (topo II).
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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