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Database: PDB
Entry: 2LJ6
LinkDB: 2LJ6
Original site: 2LJ6 
HEADER    DNA BINDING PROTEIN                     06-SEP-11   2LJ6              
TITLE     SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF THE PHOSPHOESTERASE  
TITLE    2 DOMAIN OF DNA LIGASE D                                               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PROBABLE ATP-DEPENDENT DNA LIGASE;                         
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 1-177;                                        
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA;                         
SOURCE   3 ORGANISM_TAXID: 287;                                                 
SOURCE   4 GENE: PA2138;                                                        
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_VECTOR: PET28B+                                    
KEYWDS    PHOSPHOESTERASE, DNA BINDING PROTEIN                                  
EXPDTA    SOLUTION NMR                                                          
NUMMDL    15                                                                    
AUTHOR    K.DUTTA,A.NATARAJAN,S.SHUMAN,R.GHOSE                                  
REVDAT   2   28-MAR-12 2LJ6    1       JRNL                                     
REVDAT   1   16-NOV-11 2LJ6    0                                                
JRNL        AUTH   A.NATARAJAN,K.DUTTA,D.B.TEMEL,P.A.NAIR,S.SHUMAN,R.GHOSE      
JRNL        TITL   SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF THE         
JRNL        TITL 2 PHOSPHOESTERASE DOMAIN OF DNA LIGASE D.                      
JRNL        REF    NUCLEIC ACIDS RES.            V.  40  2076 2012              
JRNL        REFN                   ISSN 0305-1048                               
JRNL        PMID   22084199                                                     
JRNL        DOI    10.1093/NAR/GKR950                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : ARIA 2.3                                             
REMARK   3   AUTHORS     : LINGE, O'DONOGHUE AND NILGES                         
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2LJ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-11.                  
REMARK 100 THE RCSB ID CODE IS RCSB102446.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 200                                
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 300 UM [U-100% 15N] PAE177, 10 %   
REMARK 210                                   D20, 90 % H20, 50 MM BIS-TRIS,     
REMARK 210                                   200 MM NACL, 5 MM DTT, 90% H2O/    
REMARK 210                                   10% D2O; 300 UM [U-100% 13C; U-    
REMARK 210                                   100% 15N] PAE177, 10 % D20, 90 %   
REMARK 210                                   H20, 50 MM BIS-TRIS, 200 MM NACL,  
REMARK 210                                   5 MM DTT, 90% H2O/10% D2O; 300 UM  
REMARK 210                                   [U-13C; U-15N; U-2H] PAE177, 10 %  
REMARK 210                                   D20, 90 % H20, 50 MM BIS-TRIS,     
REMARK 210                                   200 MM NACL, 5 MM DTT, 90% H2O/    
REMARK 210                                   10% D2O                            
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 3D HNCACB; 3D      
REMARK 210                                   HNCO; 3D TROSY; 3D HNCOCACB; 3D    
REMARK 210                                   HNCACO; 3D CC(CO)NH; 3D HC(CO)NH;  
REMARK 210                                   3D HBHACONH; 3D 1H-15N NOESY; 3D   
REMARK 210                                   1H-13C NOESY ALIPHATIC; 3D 1H-13C  
REMARK 210                                   NOESY AROMATIC                     
REMARK 210  SPECTROMETER FIELD STRENGTH    : 900 MHZ; 800 MHZ; 700 MHZ; 600     
REMARK 210                                   MHZ                                
REMARK 210  SPECTROMETER MODEL             : AVANCE; INOVA                      
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER; VARIAN                     
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : ARIA 2.3, NMRVIEW 8.1.27           
REMARK 210   METHOD USED                   : DGSA-DISTANCE GEOMETRY,            
REMARK 210                                   SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 2048                               
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 15                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST ENERGY  
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: ALL BACKBONE EXPERIMENTS WERE TROSY BASED                    
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-15                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     MET A     1                                                      
REMARK 465     PRO A     2                                                      
REMARK 465     SER A     3                                                      
REMARK 465     SER A     4                                                      
REMARK 465     LYS A     5                                                      
REMARK 465     PRO A     6                                                      
REMARK 465     LEU A     7                                                      
REMARK 465     ALA A     8                                                      
REMARK 465     GLU A     9                                                      
REMARK 465     TYR A    10                                                      
REMARK 465     ALA A    11                                                      
REMARK 465     ARG A    12                                                      
REMARK 465     LYS A    13                                                      
REMARK 465     ARG A    14                                                      
REMARK 465     ASP A    15                                                      
REMARK 465     PHE A    16                                                      
REMARK 465     ARG A    17                                                      
REMARK 465     GLN A    18                                                      
REMARK 465     THR A    19                                                      
REMARK 465     PRO A    20                                                      
REMARK 465     GLU A    21                                                      
REMARK 465     PRO A    22                                                      
REMARK 465     SER A    23                                                      
REMARK 465     GLY A    24                                                      
REMARK 465     ARG A    25                                                      
REMARK 465     LYS A    26                                                      
REMARK 465     PRO A    27                                                      
REMARK 465     ARG A    28                                                      
REMARK 465     LYS A    29                                                      
REMARK 465     ASP A    30                                                      
REMARK 465     SER A    31                                                      
REMARK 465     THR A    32                                                      
REMARK 465     GLU A   164                                                      
REMARK 465     ALA A   165                                                      
REMARK 465     ARG A   166                                                      
REMARK 465     SER A   167                                                      
REMARK 465     LEU A   168                                                      
REMARK 465     ASP A   169                                                      
REMARK 465     ARG A   170                                                      
REMARK 465     PHE A   171                                                      
REMARK 465     ASP A   172                                                      
REMARK 465     VAL A   173                                                      
REMARK 465     LEU A   174                                                      
REMARK 465     LYS A   175                                                      
REMARK 465     GLU A   176                                                      
REMARK 465     ARG A   177                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   HG   CYS A    69     OD2  ASP A    71              1.55            
REMARK 500   O    GLU A   121     H    LYS A   125              1.57            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500  1 LEU A  34     -138.54    -82.24                                   
REMARK 500  1 ALA A  44     -156.65    167.20                                   
REMARK 500  1 ASP A  56       46.60     31.78                                   
REMARK 500  1 VAL A  64      175.80    -59.85                                   
REMARK 500  1 LEU A  70      -80.24    -75.39                                   
REMARK 500  1 ASP A  71      160.82     69.30                                   
REMARK 500  1 ALA A  73      -26.08    169.10                                   
REMARK 500  1 VAL A  74       51.50   -115.62                                   
REMARK 500  1 LYS A  75      119.44    -36.95                                   
REMARK 500  1 ASP A  87      -27.53     74.85                                   
REMARK 500  1 GLU A  92      -60.10    -92.88                                   
REMARK 500  1 SER A  94     -161.30     64.95                                   
REMARK 500  1 HIS A  99      -73.90    -60.20                                   
REMARK 500  1 TYR A 100       23.87   -155.54                                   
REMARK 500  1 ALA A 102      -63.94   -174.11                                   
REMARK 500  1 ASP A 117     -144.46   -132.65                                   
REMARK 500  1 LYS A 151      -78.58    -85.95                                   
REMARK 500  1 GLN A 152      -48.68   -175.14                                   
REMARK 500  1 LYS A 161       73.94   -112.66                                   
REMARK 500  2 LEU A  34     -139.80    -81.52                                   
REMARK 500  2 ASP A  43       96.72     75.83                                   
REMARK 500  2 ALA A  44      -81.22     63.76                                   
REMARK 500  2 SER A  45      -60.49   -145.50                                   
REMARK 500  2 LEU A  47      -62.38   -100.83                                   
REMARK 500  2 TYR A  49     -102.16   -165.32                                   
REMARK 500  2 LYS A  66       78.00   -179.45                                   
REMARK 500  2 LEU A  70      -79.99    -73.74                                   
REMARK 500  2 ASP A  71      160.50     69.19                                   
REMARK 500  2 ALA A  73      -27.84    174.77                                   
REMARK 500  2 VAL A  74       57.87   -111.88                                   
REMARK 500  2 LYS A  75      112.63    -39.49                                   
REMARK 500  2 LEU A  77       99.30    -53.11                                   
REMARK 500  2 ASP A  87        4.91     82.92                                   
REMARK 500  2 TYR A  88       49.90    -88.73                                   
REMARK 500  2 ASP A  90      -73.05   -100.12                                   
REMARK 500  2 SER A  94     -110.34     78.58                                   
REMARK 500  2 ALA A 102      -81.99   -169.37                                   
REMARK 500  2 ASP A 117     -139.67   -117.46                                   
REMARK 500  2 SER A 138      177.88    177.79                                   
REMARK 500  2 ARG A 149      120.33     68.39                                   
REMARK 500  2 LYS A 151      -82.80    -82.09                                   
REMARK 500  2 GLN A 152      -43.35    179.54                                   
REMARK 500  2 SER A 153       -7.53   -142.58                                   
REMARK 500  3 LEU A  34     -137.79    -80.89                                   
REMARK 500  3 ASP A  43      148.12     85.77                                   
REMARK 500  3 TYR A  49      -89.85   -160.72                                   
REMARK 500  3 LYS A  66      139.42    157.31                                   
REMARK 500  3 LEU A  70     -117.26    -82.90                                   
REMARK 500  3 ASP A  71      154.80    162.70                                   
REMARK 500  3 LEU A  77       89.28    -68.21                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     321 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 17283   RELATED DB: BMRB                                 
DBREF  2LJ6 A    1   177  UNP    Q9I1X7   Q9I1X7_PSEAE     1    177             
SEQRES   1 A  177  MET PRO SER SER LYS PRO LEU ALA GLU TYR ALA ARG LYS          
SEQRES   2 A  177  ARG ASP PHE ARG GLN THR PRO GLU PRO SER GLY ARG LYS          
SEQRES   3 A  177  PRO ARG LYS ASP SER THR GLY LEU LEU ARG TYR CYS VAL          
SEQRES   4 A  177  GLN LYS HIS ASP ALA SER ARG LEU HIS TYR ASP PHE ARG          
SEQRES   5 A  177  LEU GLU LEU ASP GLY THR LEU LYS SER TRP ALA VAL PRO          
SEQRES   6 A  177  LYS GLY PRO CYS LEU ASP PRO ALA VAL LYS ARG LEU ALA          
SEQRES   7 A  177  VAL GLN VAL GLU ASP HIS PRO LEU ASP TYR ALA ASP PHE          
SEQRES   8 A  177  GLU GLY SER ILE PRO GLN GLY HIS TYR GLY ALA GLY ASP          
SEQRES   9 A  177  VAL ILE VAL TRP ASP ARG GLY ALA TRP THR PRO LEU ASP          
SEQRES  10 A  177  ASP PRO ARG GLU GLY LEU GLU LYS GLY HIS LEU SER PHE          
SEQRES  11 A  177  ALA LEU ASP GLY GLU LYS LEU SER GLY ARG TRP HIS LEU          
SEQRES  12 A  177  ILE ARG THR ASN LEU ARG GLY LYS GLN SER GLN TRP PHE          
SEQRES  13 A  177  LEU VAL LYS ALA LYS ASP GLY GLU ALA ARG SER LEU ASP          
SEQRES  14 A  177  ARG PHE ASP VAL LEU LYS GLU ARG                              
HELIX    1   1 ASP A   87  ALA A   89  5                                   3    
HELIX    2   2 ASP A  118  GLY A  126  1                                   9    
SHEET    1   A10 PHE A  91  ILE A  95  0                                        
SHEET    2   A10 GLY A 103  PRO A 115 -1  O  VAL A 105   N  GLY A  93           
SHEET    3   A10 HIS A 127  GLY A 134 -1  O  ASP A 133   N  ALA A 112           
SHEET    4   A10 TRP A 141  ARG A 145 -1  O  LEU A 143   N  LEU A 128           
SHEET    5   A10 TRP A 155  LYS A 159 -1  O  VAL A 158   N  HIS A 142           
SHEET    6   A10 ARG A  76  HIS A  84 -1  N  ARG A  76   O  LEU A 157           
SHEET    7   A10 THR A  58  ALA A  63 -1  N  SER A  61   O  VAL A  81           
SHEET    8   A10 HIS A  48  LEU A  55 -1  N  LEU A  55   O  THR A  58           
SHEET    9   A10 LEU A  35  HIS A  42 -1  N  HIS A  42   O  HIS A  48           
SHEET   10   A10 GLY A 103  PRO A 115 -1  O  GLY A 111   N  TYR A  37           
CISPEP   1 VAL A   64    PRO A   65          1         5.53                     
CISPEP   2 ASP A   71    PRO A   72          1        -0.43                     
CISPEP   3 VAL A   64    PRO A   65          2         7.29                     
CISPEP   4 ASP A   71    PRO A   72          2         0.42                     
CISPEP   5 VAL A   64    PRO A   65          3        12.27                     
CISPEP   6 ASP A   71    PRO A   72          3        -9.57                     
CISPEP   7 VAL A   64    PRO A   65          4        10.27                     
CISPEP   8 ASP A   71    PRO A   72          4         5.78                     
CISPEP   9 VAL A   64    PRO A   65          5        11.27                     
CISPEP  10 ASP A   71    PRO A   72          5         0.58                     
CISPEP  11 VAL A   64    PRO A   65          6        12.58                     
CISPEP  12 ASP A   71    PRO A   72          6        -1.00                     
CISPEP  13 VAL A   64    PRO A   65          7        15.35                     
CISPEP  14 ASP A   71    PRO A   72          7       -13.59                     
CISPEP  15 VAL A   64    PRO A   65          8         9.51                     
CISPEP  16 ASP A   71    PRO A   72          8         2.36                     
CISPEP  17 VAL A   64    PRO A   65          9        21.98                     
CISPEP  18 ASP A   71    PRO A   72          9        10.30                     
CISPEP  19 VAL A   64    PRO A   65         10         3.46                     
CISPEP  20 ASP A   71    PRO A   72         10        -0.69                     
CISPEP  21 VAL A   64    PRO A   65         11        11.24                     
CISPEP  22 ASP A   71    PRO A   72         11         7.31                     
CISPEP  23 VAL A   64    PRO A   65         12        14.75                     
CISPEP  24 ASP A   71    PRO A   72         12         2.55                     
CISPEP  25 VAL A   64    PRO A   65         13        10.00                     
CISPEP  26 ASP A   71    PRO A   72         13         1.63                     
CISPEP  27 VAL A   64    PRO A   65         14        19.27                     
CISPEP  28 ASP A   71    PRO A   72         14       -13.65                     
CISPEP  29 VAL A   64    PRO A   65         15        20.35                     
CISPEP  30 ASP A   71    PRO A   72         15         6.67                     
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000                         
MODEL        1                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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