Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF RECJ COMPLEXED WITH DNA
 
Authors :  Y. Hua, Y. Zhao, K. Cheng
Date :  04 Dec 15  (Deposition) - 15 Jun 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Recf Pathway, Dna End Resection, Two-Metal-Ion Catalysis, Single- Strand-Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Cheng, H. Xu, X. Chen, L. Wang, B. Tian, Y. Zhao, Y. Hua
Structural Basis For Dna 5 -End Resection By Recj
Elife V. 5 14294 2016
PubMed-ID: 27058167  |  Reference-DOI: 10.7554/ELIFE.14294

(-) Compounds

Molecule 1 - SINGLE-STRANDED-DNA-SPECIFIC EXONUCLEASE
    Atcc: ATCC13939
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28
    Expression System Strain: BL21(DE3) ROSSETTA
    Expression System Taxid: 562
    Gene: RECJ
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
 
Molecule 2 - DNA (5'-D(*GP*AP*TP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2SO47Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:439 , TRP A:663binding site for residue SO4 A 801
2AC2SOFTWAREARG A:109 , GLY A:348 , SER A:371 , ARG A:373 , DG C:194binding site for residue SO4 A 802
3AC3SOFTWARETHR A:263 , ARG A:265 , ARG A:462binding site for residue SO4 A 803
4AC4SOFTWAREGLY A:627 , PRO A:628 , LYS A:629 , THR A:630binding site for residue SO4 A 804
5AC5SOFTWARELEU A:8 , ARG A:432 , GLY A:540binding site for residue SO4 A 805
6AC6SOFTWARESER A:606 , ARG A:609binding site for residue SO4 A 806
7AC7SOFTWARETHR A:472 , ARG A:487binding site for residue SO4 A 807
8AC8SOFTWAREASP A:79 , ASP A:81 , ASP A:135 , DA C:195binding site for residue MN A 808
9AC9SOFTWAREASP A:83 , ASP A:135 , HIS A:159 , ASP A:223 , DA C:195binding site for residue MN A 809

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F55)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:454 -Pro A:455

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F55)

(-) Exons   (0, 0)

(no "Exon" information available for 5F55)

(-) 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:705
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh..eeeee..............hhhhhhhhh.eeee......hhhhhhhhhhh..eeeee............eee...............hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhhhh..eeeee..eeeee.....hhhhhhhh....eeeeee...eeeeee...hhhhhhhhhhhhhhh......eeee.ee.hhhhhhhhhhhhhhhhh..........eeeeeeeeeeeee.....eeeeee..eeeee........eeeeeeeeeeeehhhhh.eeeeeeeeeee....ee.............hhhhhhhhhhh..eee.hhhhhhhhhhhh...............eeee....hhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f55 A   1 MSRPAHWLLAPPASRDALLATMREWQVSPPVAQVLCGRDLRTELLALPLELTPNPALREAARHIVAAVREGKRIRIHGDYDADGVSATATLVLGLRAIGANVHGFIPHRLNEGYGIHPDRVPEHAAAADLVVTVDCGVSNLDEVKSLLATGTEVVVTDHHAPGENFPECLVVHPHLTPDYDPDRHNLTGAGVAYHLLWAVYEELGRPEPRALLPLATLGTVADVAPLLGENRALVRAGLAEMARTELPGLRALMNEKRVRQPTARDVAFILAPRINAAGRMGEADRALELLTTPSDHEAKSLAAYLEIRNQERRKIQDDMFAQALQLADPNDPALVLTHDDWHAGVMGIVASKLVETFNRPVYIVAQGKGSVRSTPGISAVQGLRESRDLLGRFGGHPGAAGFSLDPQNFGALRERIHGYVRQFPTPVPAVRLDAPLPVAALTPELLSELSILEPFGEGNPRPLWHLRGPLTDTRLVGKQGDVLQFRFGGVKGMKYSERDDAAGERDVAAELALNEWKGRTSLELHAAALRPLAPLALAGTEEGLPTLPRLNPREAMTFLKTGAAAYAEQGVATYLRDNVPGLTLLDTNAPHPGGDLILYGLPPESALRRWLHEAQEQGGRVAFALGPKTLAELDAALTLAKLLPDSHTEAAQEAAADAYRSWQWAHHYRVLNDAGWSASVYAMLGLPVPAALPKAAEALALAAG 705
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700     


Chain C from PDB  Type:DNA  Length:14
                                              
                 5f55 C 194 GATGTACGCTAGGC 207
                                   203
   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 5F55)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F55)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:454 - Pro A:455   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5f55
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  D0EM60_DEIRD | D0EM60
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  D0EM60_DEIRD | D0EM60
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D0EM60_DEIRD | D0EM60: 5f54 5f56

(-) Related Entries Specified in the PDB File

5f54 5f56