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(-) Description

Title :  STRUCTURE OF THE GENOME PACKAGING NTPASE B204 FROM SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS 2 IN COMPLEX WITH SULFATE
 
Authors :  L. J. Happonen, E. Oksanen, A. Goldman, T. Kajander, S. Butcher
Date :  27 Apr 13  (Deposition) - 22 May 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ftsk-Hera Superfamily, P-Loop Atpase, Genome Packaging Ntpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Happonen, E. Oksanen, L. Liljeroos, A. Goldman, T. Kajander, S. J. Butcher
The Structure Of The Ntpase That Powers Dna Packaging Into Sulfolobus Turreted Icosahedral Virus 2.
J. Virol. V. 87 8388 2013
PubMed-ID: 23698307  |  Reference-DOI: 10.1128/JVI.00831-13

(-) Compounds

Molecule 1 - GENOME PACKAGING NTPASE B204
    Chains: A, B, C
    EC Number: 3.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: ER2566/PTF16
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B204, STIV2_B204
    Organism Common: STIV2
    Organism Scientific: SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS 2
    Organism Taxid: 754004

 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, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:13 , LYS A:14 , SER A:15 , GLY A:16 , LYS A:17 , SER A:18 , HOH A:402 , HOH A:414BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREHIS A:23 , PRO A:27 , GLU A:206 , HIS A:207 , LYS C:83BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWARELYS B:13 , LYS B:14 , SER B:15 , GLY B:16 , LYS B:17 , SER B:18 , HOH B:488 , HOH B:494 , HOH B:495 , HOH B:516BINDING SITE FOR RESIDUE SO4 B 301
04AC4SOFTWARELYS A:83 , HIS B:23 , PRO B:27 , GLU B:206 , HIS B:207BINDING SITE FOR RESIDUE SO4 B 302
05AC5SOFTWARELYS B:93 , HOH B:441 , LYS C:184 , GLN C:185BINDING SITE FOR RESIDUE SO4 B 303
06AC6SOFTWAREHIS A:124 , SER B:173 , ALA B:174 , GLU B:175 , HOH B:510 , HOH B:511 , HOH B:531 , HOH B:534 , HOH B:574BINDING SITE FOR RESIDUE SO4 B 304
07AC7SOFTWAREHOH B:487 , HOH B:494 , HOH B:495 , HOH B:496 , HOH B:522 , HOH B:539BINDING SITE FOR RESIDUE MG B 305
08AC8SOFTWARETYR C:111 , ARG C:166 , TRP C:167 , LYS C:170 , TYR C:171BINDING SITE FOR RESIDUE SO4 C 301
09AC9SOFTWAREARG C:12 , LYS C:13 , LYS C:14 , SER C:15 , GLY C:16 , LYS C:17 , SER C:18 , HOH C:487 , HOH C:491 , HOH C:493BINDING SITE FOR RESIDUE SO4 C 302
10BC1SOFTWARELYS B:83 , HIS C:23 , PRO C:27 , GLU C:206 , HIS C:207 , HOH C:445 , HOH C:484 , HOH C:516 , HOH C:543BINDING SITE FOR RESIDUE SO4 C 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His B:207 -His B:208
2Met C:1 -Asn C:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KFR)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhhhh..eeeeee......hhhhheee.hhhhhhhh.eeeee......hhhhhhhhhhhhhhhhhh.eeeee.hhhhh.......hhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhh......eeeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfr A   1 MNPDDIVVLVGRKKSGKSYLIKHYFIPVLKAHKISYIIDDHNLGSEYSKFGYNATSLSDIVSKQYVVVYDRAKNDDFFEKLWQASKLHSKKYGTTVLIIDEAYYHFKYKQKVTPAIDEALHANRHAGLGLILSTQRVYDLMPIVYKQADLIIMFYTREPNELRWISKYISAEAAEKVKTLKQYHFLIYDVNSQTIKIHKPILEHH 208
                                    10        20        30        40  ||    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     
                                                                     43|                                                                                                                                                                 
                                                                      47                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeee.....hhhhhhhhhhhhhhhhh..eeeeee..hhhhh..hhhhhee..hhhhhhhh.eeeee......hhhhhhhhhhhhhhhhhh.eeeee..hhhhhh.....hhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhh......eeeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfr B   1 MNPDDIVVLVGRKKSGKSYLIKHYFIPVLKAHKISYIIDDHNLLRSGSEYSKFGYNATSLSDIVSKQYVVVYDRAKNDDFFEKLWQASKLHSKKYGTTVLIIDEAYYHFKYKQKVTPAIDEALHANRHAGLGLILSTQRVYDLMPIVYKQADLIIMFYTREPNELRWISKYISAEAAEKVKTLKQYHFLIYDVNSQTIKIHKPILEHH 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhhhhhhh..eeeeee......hhhhheee.hhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhh.eeeee..hhhhhh.....hhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfr C   1 MNPDDIVVLVGRKKSGKSYLIKHYFIPVLKAHKISYIIDDHNLGSEYSKFGYNATSLSDIVSKQYVVVYDDDFFEKLWQASKLHSKKYGTTVLIIDEAYYHFKYKQKVTPAIDEALHANRHAGLGLILSTQRVYDLMPIVYKQADLIIMFYTREPNELRWISKYISAEAAEKVKTLKQYHFLIYDVNSQTIKIHKPILEH 207
                                    10        20        30        40  ||    53        63        73|       87        97       107       117       127       137       147       157       167       177       187       197       207
                                                                     43|                        73|                                                                                                                                 
                                                                      47                         78
   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 4KFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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        D5IEZ9_9VIRU | D5IEZ9: 4kfs 4kft 4kfu

(-) Related Entries Specified in the PDB File

4kfs STRUCTURE OF THE GENOME PACKAGING NTPASE B204 FROM SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS 2 IN COMPLEX WITH AMP
4kft STRUCTURE OF THE GENOME PACKAGING NTPASE B204 FROM SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS 2 IN COMPLEX WITH ATPGAMMAS
4kfu STRUCTURE OF THE GENOME PACKAGING NTPASE B204 FROM SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS 2 IN COMPLEX WITH AMPPCP