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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DNA BINDING PROTEIN (BT_1116) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 Jun 09  (Deposition) - 30 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Duf269 Family Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Dna Binding Protein (Np_810029. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DNA BINDING PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 38-185
    Gene: BT_1116, NP_810029.1
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
11PE5Ligand/IonPENTAETHYLENE GLYCOL
2FE1Ligand/IonFE (III) ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
4NI2Ligand/IonNICKEL (II) ION
5SO48Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:131 , HIS A:133 , HIS A:147 , HOH A:410 , HOH C:619BINDING SITE FOR RESIDUE NI A 201
02AC2SOFTWARELYS A:106 , PHE A:108 , ARG A:138 , HOH A:294 , HOH A:304 , HOH A:398 , HOH B:524 , ASN C:97 , THR C:100 , ALA C:102 , HOH C:737BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREASN A:52 , LYS A:53 , GLU A:162 , ASN B:52 , LYS B:53 , ASN C:52 , LYS C:53BINDING SITE FOR RESIDUE SO4 A 203
04AC4SOFTWARESER A:123 , MSE A:124 , ASN A:125 , GLU A:126 , ARG A:167 , SER A:169 , HOH A:271 , HOH A:335BINDING SITE FOR RESIDUE SO4 A 204
05AC5SOFTWAREARG A:94 , TYR A:103 , TYR A:129 , HIS A:147 , HOH A:287BINDING SITE FOR RESIDUE 1PE A 205
06AC6SOFTWAREASN A:60 , HIS A:61 , HOH A:352 , LEU B:176BINDING SITE FOR RESIDUE 1PE A 206
07AC7SOFTWAREHOH A:269 , HIS B:131 , HIS B:133 , HIS B:147 , HOH B:519 , HOH B:528BINDING SITE FOR RESIDUE FE B 207
08AC8SOFTWAREHIS B:61 , HOH B:500BINDING SITE FOR RESIDUE NI B 208
09AC9SOFTWARELYS B:106 , PHE B:108 , ARG B:138 , 1PE B:212 , HOH B:531 , HOH B:567BINDING SITE FOR RESIDUE SO4 B 209
10BC1SOFTWAREASN B:125 , ARG B:167 , SER B:169 , ARG B:185 , HOH B:473 , HOH B:494 , HOH B:571BINDING SITE FOR RESIDUE SO4 B 210
11BC2SOFTWARELYS B:49 , TYR B:54 , LYS B:75 , HOH B:573BINDING SITE FOR RESIDUE SO4 B 211
12BC3SOFTWAREGLU B:110 , ARG B:138 , SER B:139 , ASP B:140 , SO4 B:209 , HOH B:584BINDING SITE FOR RESIDUE 1PE B 212
13BC4SOFTWAREMSE C:124 , ASN C:125 , ARG C:167 , SER C:169 , ARG C:185 , HOH C:622 , HOH C:673BINDING SITE FOR RESIDUE SO4 C 213
14BC5SOFTWAREASN A:97 , THR A:100 , ALA A:102 , HOH A:353 , LYS C:106 , ARG C:138 , HOH C:655 , HOH C:671 , HOH C:697 , HOH C:743 , HOH C:758BINDING SITE FOR RESIDUE SO4 C 214
15BC6SOFTWAREARG A:109 , ARG C:94 , PHE C:96 , TYR C:103 , TYR C:129 , HIS C:147BINDING SITE FOR RESIDUE 1PE C 215
16BC7SOFTWARETYR C:47 , LYS C:49 , TYR C:54 , LYS C:75 , HOH C:677BINDING SITE FOR RESIDUE 1PE C 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HTN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HTN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HTN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HTN)

(-) Exons   (0, 0)

(no "Exon" information available for 3HTN)

(-) 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:143
 aligned with Q8A8Q1_BACTN | Q8A8Q1 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         Q8A8Q1_BACTN    43 NMYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQMEISNLTGNISSMNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER 185
               SCOP domains d3htna_ A: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee....hhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee......eeeeee...eeeeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee.....eeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3htn A  43 NmYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQmEISNLTGNISSmNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER 185
                             |      52        62        72        82        92       102       112       122 |     132       142       152       162       172       182   
                             |                                                                 112-MSE     124-MSE                                                         
                            44-MSE                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:139
 aligned with Q8A8Q1_BACTN | Q8A8Q1 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         Q8A8Q1_BACTN    43 NMYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQMEISNLTGNISSMNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER 185
               SCOP domains d3htnb_ B: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee....hhhhhhhhhhhhh....eeeeeeeeeeeeeee.....----.eeee...eeeeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee.....eeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3htn B  43 NmYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPK----DDKTFREQmEISNLTGNISSmNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER 185
                             |      52        62        72        82        92      |  - |     112       122 |     132       142       152       162       172       182   
                            44-MSE                                                 99  104     112-MSE     124-MSE                                                         


Chain C from PDB  Type:PROTEIN  Length:143
 aligned with Q8A8Q1_BACTN | Q8A8Q1 from UniProtKB/TrEMBL  Length:185

    Alignment length:143
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182   
         Q8A8Q1_BACTN    43 NMYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQMEISNLTGNISSMNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER 185
               SCOP domains d3htnc_ C: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee....hhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee......eeeeee...eeeeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee.....eeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3htn C  43 NmYSYKKIGNKYIVSINNHTEIVKALNAFCKEKGILSGSINGIGAIGELTLRFFNPKTKAYDDKTFREQmEISNLTGNISSmNEQVYLHLHITVGRSDYSALAGHLLSAIQNGAGEFVVEDYSERISRTYNPDLGLNIYDFER 185
                             |      52        62        72        82        92       102       112       122 |     132       142       152       162       172       182   
                            44-MSE                                                             112-MSE     124-MSE
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HTN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HTN)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q8A8Q1_BACTN | Q8A8Q1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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