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(-) Description

Title :  ENTEROBACTERIA PHAGE T4 GP5.4 PAAR REPEAT PROTEIN IN COMPLEX WITH T4 GP5 BETA-HELIX FRAGMENT
 
Authors :  S. A. Buth, P. G. Leiman, M. M. Shneider
Date :  21 May 13  (Deposition) - 21 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Paar-Repeat Motif, Membrane Piercing, Type Vi Secretion System, T6Ss, Cell Puncturing Device, Beta-Helix, Gp5-Gp27 Protein Complex, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Buth, P. G. Leiman, M. M. Shneider
Crystall Structute Of The Business End Of The T4 Cell-Puncturing Device
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TAIL-ASSOCIATED LYSOZYME
    Chains: A, B, C
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEEVA2, A PET23A DERIVATIVE
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 484-575
    Gene: 5
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: PROTEIN GP5, GP5C
 
Molecule 2 - UNCHARACTERIZED 10.2 KDA PROTEIN IN SEGC-GP6 INTERGENIC REGION
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEEVA2, A PET23A DERIVATIVE
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 5.4, Y08B
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: GP5.4

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric/Biological Unit (7, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ELA1Ligand/Ion9-OCTADECENOIC ACID
3FE1Ligand/IonFE (III) ION
4MG1Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION
6PLM1Ligand/IonPALMITIC ACID
7STE1Ligand/IonSTEARIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:705 , HOH A:764 , HOH B:712 , HOH B:721 , HOH C:718 , HOH C:726BINDING SITE FOR RESIDUE MG A 601
02AC2SOFTWAREILE A:496 , VAL A:502 , ILE A:504 , THR A:520 , GLN A:526 , HOH A:811 , ILE B:504 , GLY C:494 , ILE C:496BINDING SITE FOR RESIDUE ELA A 602
03AC3SOFTWARESER A:561 , HOH A:701 , HOH A:760 , HOH A:769 , HOH A:813 , HOH A:814 , ASP B:568BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWARETHR A:495 , VAL A:514 , ALA A:518 , THR A:520 , ILE B:504 , GLN B:526 , HOH B:747 , GLU C:486 , ILE C:504BINDING SITE FOR RESIDUE STE B 601
05AC5SOFTWAREILE A:504 , ILE A:512 , GLY B:494 , THR B:495 , VAL B:514 , VAL C:502 , ILE C:504 , GLN C:526BINDING SITE FOR RESIDUE PLM C 601
06AC6SOFTWAREARG C:571 , ASP C:573 , HOH C:772 , TYR D:68BINDING SITE FOR RESIDUE EDO C 602
07AC7SOFTWAREHIS D:14 , HIS D:46 , HIS D:56 , CYS D:83BINDING SITE FOR RESIDUE FE D 101
08AC8SOFTWAREALA D:24 , THR D:25 , GLN D:26 , VAL D:36 , ASP D:41BINDING SITE FOR RESIDUE NA D 102
09AC9SOFTWARETYR D:6 , THR D:31 , GLY D:32 , HOH D:211 , HOH D:213 , HOH D:300 , HOH D:317BINDING SITE FOR RESIDUE EDO D 103
10BC1SOFTWAREHOH A:841 , SER D:2 , ILE D:96 , HOH D:207 , HOH D:261BINDING SITE FOR RESIDUE EDO D 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KU0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys D:51 -Pro D:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KU0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KU0)

(-) Exons   (0, 0)

(no "Exon" information available for 4KU0)

(-) Sequences/Alignments

Asymmetric/Biological 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee...eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4ku0 A 484 GDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
                                   493       503       513       523       533       543       553       563       573  


Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4ku0 B 484 GDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
                                   493       503       513       523       533       543       553       563       573  


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee...eeeee..eeeeee.eeeeee..eeeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4ku0 C 484 GDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIG 575
                                   493       503       513       523       533       543       553       563       573  


Chain D from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................eee..ee..........ee.......ee..........eee..ee....................eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4ku0 D   2 SGLSYDKCVTAGHEAWPPTVVNATQSKVFTGGIAVLVAGDPITEHTEIKKPYETHGGVTQPRTSKVYVTGKKAVQMADPISCGDTVAQASSKVFIK  97
                                    11        21        31        41        51        61        71        81        91
   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 4KU0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KU0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KU0)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys D:51 - Pro D:52   [ RasMol ]  
 

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  NEEDL_BPT4 | P39234
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BP5_BPT4 | P16009: 1k28 1pdl 1wth 2z6b 3a1m 4jiv 4jiw 4jj2 4osd 5iv5
        NEEDL_BPT4 | P39234: 5iv5

(-) Related Entries Specified in the PDB File

1k28 FULL-LENGTH T4 PHAGE GP5 PROTEIN IN COMPLEX WITH GP27
4jiv VCA0105 PAAR-REPEAT PROTEIN FROM VIBRIO CHOLERAE IN COMPLEX WITH A VGRG-LIKE BETA-HELIX THAT IS BASED ON A FRAGMENT OF T4 GP5
4jiw C1882 PAAR-REPEAT PROTEIN FROM ESCHERICHIA COLI IN COMPLEX WITH A VGRG-LIKE BETA-HELIX THAT IS BASED ON A FRAGMENT OF T4 GP5
4jj2 HIGH RESOLUTION STRUCTURE OF A C-TERMINAL FRAGMENT OF THE T4 PHAGE GP5 BETA-HELIX