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(-) Description

Title :  CRYSTAL STRUCTURE OF APETHERMO-DBP-RP2
 
Authors :  H. Gahlei, H. Von Moeller, D. Eppers, B. Loll, M. C. Wahl
Date :  07 Mar 14  (Deposition) - 30 Apr 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ssdna Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ghalei, H. V. Moeller, D. Eppers, D. Sohmen, D. N. Wilson, B. Loll, M. C. Wahl
Entrapment Of Dna In An Intersubunit Tunnel System Of A Single-Stranded Dna-Binding Protein.
Nucleic Acids Res. V. 42 6698 2014
PubMed-ID: 24744237  |  Reference-DOI: 10.1093/NAR/GKU259

(-) Compounds

Molecule 1 - SSDNA BINDING PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-M11
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APE_1866.1
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IMD6Ligand/IonIMIDAZOLE
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:5 , THR A:6BINDING SITE FOR RESIDUE IMD A 301
2AC2SOFTWAREALA A:11 , VAL A:56BINDING SITE FOR RESIDUE IMD A 302
3AC3SOFTWAREARG A:160 , ARG A:208 , GLU A:212 , LEU C:170 , LEU C:171 , IMD C:301BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREALA B:11 , LYS B:63BINDING SITE FOR RESIDUE IMD B 301
5AC5SOFTWAREGOL A:303 , GLU C:212 , LEU C:216 , HOH C:456BINDING SITE FOR RESIDUE IMD C 301
6AC6SOFTWAREARG C:204 , ARG C:208 , ARG D:19BINDING SITE FOR RESIDUE IMD D 301
7AC7SOFTWAREHOH A:473 , ALA D:11 , ALA D:61 , ASP D:62 , LYS D:63 , GOL D:303BINDING SITE FOR RESIDUE IMD D 302
8AC8SOFTWAREGLU A:165 , LYS A:203 , HOH A:440 , ALA D:12 , TYR D:14 , ALA D:15 , IMD D:302 , HOH D:403BINDING SITE FOR RESIDUE GOL D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:165 -Pro A:166
2Glu B:165 -Pro B:166
3Glu C:165 -Pro C:166
4Glu D:165 -Pro D:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PSN)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee..eeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psn A   0 mLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAmAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRImYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVKA 219
                            |        9        19        29        39  |     49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
                            |                                        42-MSE                                                                                          139-MSE                                                                            
                            0-MSE                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee..eeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psn B   0 mLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAmAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRImYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                            |        9        19        29        39  |     49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
                            0-MSE                                    42-MSE                                                                                          139-MSE                                                                           


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhh..........eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psn C  -2 GAmLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAmAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRImYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                              |      7        17        27        37    |   47        57        67        77        87        97       107       117       127       137 |     147       157       167       177       187       197       207       217 
                              0-MSE                                    42-MSE                                                                                          139-MSE                                                                           


Chain D from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...ee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.........eeeeeeeeee....eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee..eeeeeeeeee...eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4psn D  -2 GAmLPTLRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAmAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQIQFDFSTLRVELWRRVPEEEIAPIVEDFARAAPRLLEEEIRFTVEKVGETDVGDVVYRImYRGSDVGALIVTPLNGEALVRGAVVEPTPLLLKRTRVQVEADRIDDFVRESVSRLFSEAQNVEKREAVRVVNEILSLVK 218
                              |      7        17        27        37    |   47        57        67        77        87        97       107       117       127       137 |     147       157       167       177       187       197       207       217 
                              0-MSE                                    42-MSE                                                                                          139-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  (0, 0)

(no "SCOP Domain" information available for 4PSN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PSN)

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  Cis Peptide Bonds
    Glu A:165 - Pro A:166   [ RasMol ]  
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        Q9YAS7_AERPE | Q9YAS7: 4pso

(-) Related Entries Specified in the PDB File

4psl 4psm 4pso