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(-) Description

Title :  STRUCTURE OF THE C2221 FORM OF PNOB8-LIKE PARB-N DOMAIN
 
Authors :  M. Schumacher
Date :  23 May 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Parb-N, Pnob8, Partition, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, N. K. Tonthat, J. Lee, F. A. Rodriguez-Castneda, N. B. Chinnam, A. K. Kalliomaa-Sanford, I. W. Ng, M. T. Barge, P. L. Shaw D. Barilla
Structures Of Archaeal Dna Segregation Machinery Reveal Bacterial And Eukaryotic Linkages.
Science V. 349 1120 2015
PubMed-ID: 26339031  |  Reference-DOI: 10.1126/SCIENCE.AAA9046

(-) Compounds

Molecule 1 - PARB DOMAIN PROTEIN NUCLEASE
    Chains: B, A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-298
    Gene: SSOL_1539
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 555311
    Strain: 98/2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 25)

Asymmetric Unit (2, 25)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:29 , ASP B:58 , GLY B:59 , TYR B:60 , THR B:61 , ARG B:62 , ASN B:98 , ARG B:101 , HOH B:404 , HOH B:406 , HOH B:408binding site for residue CIT B 301
2AC2SOFTWAREVAL A:26 , ASN A:29 , ASP A:58 , GLY A:59 , TYR A:60 , THR A:61 , ARG A:62 , ARG A:101 , HOH A:404binding site for residue CIT A 301
3AC3SOFTWARETRP C:201 , LYS C:204 , TYR C:205 , ASP C:208 , ARG C:242 , ASP C:243 , HOH C:401binding site for residue CIT C 301
4AC4SOFTWAREVAL C:26 , ASP C:58 , GLY C:59 , TYR C:60 , THR C:61 , ARG C:62 , ASN C:98 , ARG C:101binding site for residue CIT C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K5D)

(-) Exons   (0, 0)

(no "Exon" information available for 5K5D)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhh..hhhhhh........hhhhhhhhhhh....eee.....eeehhhhhhhhhhh...eeeeeee......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......hhhhh.eee.....eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k5d A   1 mTELTYTEEVVSIEKLKEDDEFKTmVPSNNSREDLEKSLREKSQIFPLIADRNYVLIDGYTRLDImKKLGFKEVKILKYDFDSQQERDKAYELIWTFNGVRRQLDKNERLALFQKIADRIAKmQASKNKTEQIEENEEFVTLDDGTTISALEYERILKELDKENKALSESDKRKmAILRINTPWLLKYVTDQKYKVPLDQAFRIYTRVKDmGILDKLKDLAPALRDPLITTREGRKIILNDEYRDLmEKIIS 269
                            |       10        20    |   30        40        50        60     |  70        80        90       100       110       120  |    130||     157       167       177       187    |  197       207       217       227|      237       247       257      |267  
                            |                      25-MSE                                   66-MSE                                                  123-MSE 131|                                        192-MSE                             228-MSE                             264-MSE 
                            1-MSE                                                                                                                            149                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhheehhhhhhh.....hhhhhhhhhhhhh....eee....eeeehhhhhhhhhhh...eeeeeee......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh........eeee.....eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k5d B   1 mTELTYTEEVVSIEKLKEDDEFKTmVPSNNSREDLEKSLREKSQIFPLIADRNYVLIDGYTRLDImKKLGFKEVKILKYDFDSQQERDKAYELIWTFNGVRRQLDKNERLALFQKIADRIAKmQASKNKTEEENEEFVTLDDGTTISALEYERILKELDKENKALSESDKRKmAILRINTPWLLKYVTDQKYKVPLDQAFRIYTRVKDmGILDKLKDLAPALRDPLITTREGRKIILNDEYRDLmEKIIS 269
                            |       10        20    |   30        40        50        60     |  70        80        90       100       110       120  |    130||     159       169       179       189  |    199       209       219       229       239       249       259    |  269
                            1-MSE                  25-MSE                                   66-MSE                                                  123-MSE 131|                                      192-MSE                             228-MSE                             264-MSE 
                                                                                                                                                             151                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee......hhhhhh....hhhhhhhhhhhhh....eee.....eeehhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..........eee.....eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k5d C   1 mTELTYTEEVVSIEKLKEDDEFKTmVNNSREDLEKSLREKSQIFPLIADRNYVLIDGYTRLDImKKLGFKEVKILKYDFDSQQERDKAYELIWTFNGVRRQLDKNERLALFQKIADRIAKmQASKNKTEIEENEEFVTLDDGTTISALEYERILKELDKENKALSESDKRKmAILRINTPWLLKYVTDQKYKVPLDQAFRIYTRVKDmGILDKLKDLAPALRDPLITTREGRKIILNDEYRDLmEKIIS 269
                            |       10        20    ||| 32        42        52        62   |    72        82        92       102       112       122|      150       160       170       180       190 |     200       210       220       230       240       250       260   |     
                            1-MSE                  25-MSE                                 66-MSE                                                  123-MSE 131|                                       192-MSE                             228-MSE                             264-MSE 
                                                    26|                                                                                                    150                                                                                                                       
                                                     29
   Legend:   → Mismatch (orange background)
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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 5K5D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K5D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5K5D)

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 Related Entries

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        D0KSP7_SULS9 | D0KSP7: 5k5a

(-) Related Entries Specified in the PDB File

5k5a