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Database: PDB
Entry: 1YHO
LinkDB: 1YHO
Original site: 1YHO 
HEADER    OXIDOREDUCTASE                          10-JAN-05   1YHO              
TITLE     SOLUTION STRUCTURE OF HUMAN DIHYDROFOLATE REDUCTASE                   
TITLE    2 COMPLEXED WITH TRIMETHOPRIM AND NADPH, 25 STRUCTURES                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DIHYDROFOLATE REDUCTASE;                                   
COMPND   3 CHAIN: A;                                                            
COMPND   4 EC: 1.5.1.3;                                                         
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: NF1;                                       
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PMT702                                    
KEYWDS    DHFR, INHIBITOR/ENZYME COMPLEX, OXIDOREDUCTASE                        
EXPDTA    SOLUTION NMR                                                          
NUMMDL    25                                                                    
MDLTYP    MINIMIZED AVERAGE                                                     
AUTHOR    V.I.POLSHAKOV,B.BIRDSALL                                              
REVDAT   2   24-FEB-09 1YHO    1       VERSN                                    
REVDAT   1   22-NOV-05 1YHO    0                                                
JRNL        AUTH   N.V.KOVALEVSKAYA,Y.D.SMURNYY,V.I.POLSHAKOV,                  
JRNL        AUTH 2 B.BIRDSALL,A.F.BRADBURY,T.FRENKIEL,J.FEENEY                  
JRNL        TITL   SOLUTION STRUCTURE OF HUMAN DIHYDROFOLATE                    
JRNL        TITL 2 REDUCTASE IN ITS COMPLEX WITH TRIMETHOPRIM AND               
JRNL        TITL 3 NADPH.                                                       
JRNL        REF    J.BIOMOL.NMR                  V.  33    69 2005              
JRNL        REFN                   ISSN 0925-2738                               
JRNL        PMID   16222560                                                     
JRNL        DOI    10.1007/S10858-005-1475-Z                                    
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS BRUNGER, ARIA                                    
REMARK   3   AUTHORS     : 1.1 (CNS), 2.0A (ARIA)                               
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HIGH TEMP (1000 K) STAGE: 30 PS           
REMARK   3  (10000 SEPS), 1000 -> 0 K COOLING (25 K STEP, 30PS TRAJECTORY       
REMARK   3  ON EACH STEP). 700 STEPS OF FINAL ENERGY OPTIMIZATION.              
REMARK   4                                                                      
REMARK   4 1YHO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-05.                  
REMARK 100 THE RCSB ID CODE IS RCSB031522.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 288                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 100 MM KCL                         
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : UNIFORM (RANDOM) LABELING          
REMARK 210                                   WITH 13C, 15N AT KNOWN             
REMARK 210                                   LABELING LEVELS: U-95% 13C, U-     
REMARK 210                                   98% 15N, 1 MM; NADPH 1MM,          
REMARK 210                                   TRIMETHOPRIME 1MM; 50MM            
REMARK 210                                   PHOSPHATE BUFFER                   
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D NOESY, 2D COSY, 15N-HSQC,       
REMARK 210                                   13C-HSQC, 13C-NOESY-HSQC, 15N-     
REMARK 210                                   NOESY-HSQC, 15N-REJECTED-          
REMARK 210                                   NOESY, 13C-REJECTED-NOESY,         
REMARK 210                                   HNCA, HNCO, HN(CO)CA, HNCACB,      
REMARK 210                                   CBCA(CO)NH, HBHA(CO)NH, HCCH-      
REMARK 210                                   TOCSY                              
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ, 600 MHZ                   
REMARK 210  SPECTROMETER MODEL             : UNITYPLUS, INOVA                   
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : VNMR VARIAN INC, NMRPIPE           
REMARK 210                                   DELAGLIO, SPARKY GODDARD           
REMARK 210   METHOD USED                   : SIMULATED ANNEALING,               
REMARK 210                                   MOLECULAR DYNAMICS                 
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 40                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 25                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: BACKBONE ASSIGMENT WAS PERFORMED USING TRIPLE-RESONANCE      
REMARK 210  NMR SPECTROSCOPY.                                                   
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 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 THR A  40       86.38    -68.87                                   
REMARK 500  1 ASP A 110      -53.13   -124.47                                   
REMARK 500  1 GLN A 140      140.08   -174.21                                   
REMARK 500  2 PRO A  25      173.64    -53.11                                   
REMARK 500  2 THR A  40       93.37    -67.97                                   
REMARK 500  2 LEU A  67       94.19    -65.65                                   
REMARK 500  2 VAL A 115      -67.21    -96.10                                   
REMARK 500  2 GLN A 140      131.31   -171.41                                   
REMARK 500  3 SER A  42       36.23    -98.71                                   
REMARK 500  3 ASP A 110      -64.47   -130.98                                   
REMARK 500  3 GLN A 140      124.05   -170.87                                   
REMARK 500  4 THR A  40       79.15    -67.25                                   
REMARK 500  4 SER A  42       36.69    -96.11                                   
REMARK 500  4 ASP A 110      -68.47   -125.71                                   
REMARK 500  4 VAL A 115      -65.88    -94.65                                   
REMARK 500  4 GLN A 140      137.72   -171.42                                   
REMARK 500  5 ASP A 110      -52.69   -130.09                                   
REMARK 500  5 GLN A 140      124.19   -170.26                                   
REMARK 500  6 LEU A  67       93.07    -62.88                                   
REMARK 500  7 THR A  40       93.77    -68.34                                   
REMARK 500  7 GLN A 140      124.48   -176.93                                   
REMARK 500  8 GLN A 140      127.62   -174.40                                   
REMARK 500  9 PRO A  25     -177.35    -55.61                                   
REMARK 500  9 THR A  40       82.08    -68.74                                   
REMARK 500  9 ASP A 110      -50.11   -138.72                                   
REMARK 500  9 GLN A 140      135.48   -174.07                                   
REMARK 500 10 ASP A 110      -57.16   -125.98                                   
REMARK 500 10 GLN A 140      135.75   -176.97                                   
REMARK 500 11 PRO A  25      172.83    -54.72                                   
REMARK 500 11 THR A  40       94.32    -67.27                                   
REMARK 500 11 VAL A 115       40.11   -109.01                                   
REMARK 500 12 GLN A 140      123.88   -176.54                                   
REMARK 500 13 PRO A  25      178.46    -53.97                                   
REMARK 500 13 THR A  40       86.86    -68.94                                   
REMARK 500 13 LEU A  67       93.87    -69.48                                   
REMARK 500 14 THR A  40       87.44    -68.70                                   
REMARK 500 14 LEU A  67       93.63    -64.40                                   
REMARK 500 15 THR A  40       93.89    -68.14                                   
REMARK 500 15 LEU A  67       96.17    -67.51                                   
REMARK 500 15 ASP A 110      -53.82   -126.80                                   
REMARK 500 16 THR A  40       95.01    -68.27                                   
REMARK 500 16 GLN A 140      130.28   -174.48                                   
REMARK 500 17 LEU A  67       98.30    -60.90                                   
REMARK 500 17 ASP A 110      -67.39   -134.60                                   
REMARK 500 17 VAL A 115       40.47   -108.70                                   
REMARK 500 17 GLN A 140      135.22   -170.03                                   
REMARK 500 18 PRO A  25      178.74    -56.40                                   
REMARK 500 18 LEU A  67       98.89    -62.66                                   
REMARK 500 18 VAL A 115      -66.12    -93.29                                   
REMARK 500 19 GLN A 140      134.41   -172.44                                   
REMARK 500 20 ASP A 110      -64.99   -128.82                                   
REMARK 500 21 PRO A  25      178.36    -54.15                                   
REMARK 500 21 THR A  40       95.99    -68.30                                   
REMARK 500 21 LEU A  67       93.78    -62.87                                   
REMARK 500 21 ASP A 110      -46.59   -130.89                                   
REMARK 500 22 PRO A  25      171.97    -53.54                                   
REMARK 500 22 THR A  40       94.80    -66.75                                   
REMARK 500 22 LEU A  67       93.60    -65.87                                   
REMARK 500 22 SER A  76      110.63   -161.24                                   
REMARK 500 22 VAL A 115      -65.69    -98.00                                   
REMARK 500 23 PRO A  25      175.41    -53.84                                   
REMARK 500 23 THR A  40       96.65    -68.44                                   
REMARK 500 23 VAL A 115      -67.11    -94.16                                   
REMARK 500 24 THR A  40       99.22    -67.81                                   
REMARK 500 24 LEU A  67       93.81    -61.92                                   
REMARK 500 24 ASP A 110      -64.60   -130.87                                   
REMARK 500 24 GLN A 140      117.57   -161.59                                   
REMARK 500 25 VAL A 115      -67.13   -102.98                                   
REMARK 500 25 GLN A 140      128.46   -170.08                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 190                 
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRR A 200                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1KMS   RELATED DB: PDB                                   
REMARK 900 HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-            
REMARK 900 ([5-QUINOLYLAMINO]METHYL)-2,4-DIAMINO-5-METHYLPYRIDO[2,3-            
REMARK 900 D]PYRIMIDINE (SRI-9439), A LIPOPHILIC ANTIFOLATE                     
REMARK 900 RELATED ID: 1KMV   RELATED DB: PDB                                   
REMARK 900 HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND (Z)-          
REMARK 900 6-(2-[2,5-DIMETHOXYPHENYL]ETHEN-1-YL)-2,4-DIAMINO-5-                 
REMARK 900 METHYLPYRIDO[2,3-D]PYRIMIDINE (SRI-9662), A LIPOPHILIC               
REMARK 900 ANTIFOLATE                                                           
REMARK 900 RELATED ID: 1LUD   RELATED DB: PDB                                   
REMARK 900 L.CASEI DIHYDROFOLATE REDUCTASE COMPLEXED WITH                       
REMARK 900 TRIMETHOPRIME AND NADPH                                              
DBREF  1YHO A    1   186  UNP    P00374   DYR_HUMAN        1    186             
SEQRES   1 A  186  VAL GLY SER LEU ASN CYS ILE VAL ALA VAL SER GLN ASN          
SEQRES   2 A  186  MET GLY ILE GLY LYS ASN GLY ASP LEU PRO TRP PRO PRO          
SEQRES   3 A  186  LEU ARG ASN GLU PHE ARG TYR PHE GLN ARG MET THR THR          
SEQRES   4 A  186  THR SER SER VAL GLU GLY LYS GLN ASN LEU VAL ILE MET          
SEQRES   5 A  186  GLY LYS LYS THR TRP PHE SER ILE PRO GLU LYS ASN ARG          
SEQRES   6 A  186  PRO LEU LYS GLY ARG ILE ASN LEU VAL LEU SER ARG GLU          
SEQRES   7 A  186  LEU LYS GLU PRO PRO GLN GLY ALA HIS PHE LEU SER ARG          
SEQRES   8 A  186  SER LEU ASP ASP ALA LEU LYS LEU THR GLU GLN PRO GLU          
SEQRES   9 A  186  LEU ALA ASN LYS VAL ASP MET VAL TRP ILE VAL GLY GLY          
SEQRES  10 A  186  SER SER VAL TYR LYS GLU ALA MET ASN HIS PRO GLY HIS          
SEQRES  11 A  186  LEU LYS LEU PHE VAL THR ARG ILE MET GLN ASP PHE GLU          
SEQRES  12 A  186  SER ASP THR PHE PHE PRO GLU ILE ASP LEU GLU LYS TYR          
SEQRES  13 A  186  LYS LEU LEU PRO GLU TYR PRO GLY VAL LEU SER ASP VAL          
SEQRES  14 A  186  GLN GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU VAL TYR          
SEQRES  15 A  186  GLU LYS ASN ASP                                              
HET    NDP  A 190      74                                                       
HET    TRR  A 200      40                                                       
HETNAM     NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE                  
HETNAM   2 NDP  PHOSPHATE                                                       
HETNAM     TRR 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-             
HETNAM   2 TRR  IUM                                                             
FORMUL   2  NDP    C21 H30 N7 O17 P3                                            
FORMUL   3  TRR    C14 H19 N4 O3 1+                                             
HELIX    1   1 LEU A   27  THR A   40  1                                  14    
HELIX    2   2 LYS A   54  ILE A   60  1                                   7    
HELIX    3   3 SER A   92  GLN A  102  1                                  11    
HELIX    4   4 GLN A  102  ASN A  107  1                                   6    
HELIX    5   5 GLY A  117  MET A  125  1                                   9    
SHEET    1   A 8 PHE A  88  SER A  90  0                                        
SHEET    2   A 8 ILE A  71  LEU A  75  1  N  VAL A  74   O  PHE A  88           
SHEET    3   A 8 GLN A  47  GLY A  53  1  N  MET A  52   O  LEU A  73           
SHEET    4   A 8 VAL A 109  ILE A 114  1  O  TRP A 113   N  LEU A  49           
SHEET    5   A 8 SER A   3  SER A  11  1  N  ASN A   5   O  ILE A 114           
SHEET    6   A 8 LEU A 131  MET A 139  1  O  THR A 136   N  VAL A  10           
SHEET    7   A 8 ILE A 175  LYS A 184 -1  O  TYR A 182   N  LEU A 133           
SHEET    8   A 8 TYR A 156  LEU A 159 -1  N  LEU A 159   O  VAL A 181           
SHEET    1   B 8 PHE A  88  SER A  90  0                                        
SHEET    2   B 8 ILE A  71  LEU A  75  1  N  VAL A  74   O  PHE A  88           
SHEET    3   B 8 GLN A  47  GLY A  53  1  N  MET A  52   O  LEU A  73           
SHEET    4   B 8 VAL A 109  ILE A 114  1  O  TRP A 113   N  LEU A  49           
SHEET    5   B 8 SER A   3  SER A  11  1  N  ASN A   5   O  ILE A 114           
SHEET    6   B 8 LEU A 131  MET A 139  1  O  THR A 136   N  VAL A  10           
SHEET    7   B 8 ILE A 175  LYS A 184 -1  O  TYR A 182   N  LEU A 133           
SHEET    8   B 8 GLN A 170  GLU A 172 -1  N  GLU A 172   O  ILE A 175           
SHEET    1   C 2 GLY A  15  GLY A  17  0                                        
SHEET    2   C 2 THR A 146  PHE A 147 -1  O  THR A 146   N  GLY A  17           
CISPEP   1 ARG A   65    PRO A   66          1        -7.24                     
CISPEP   2 GLY A  116    GLY A  117          1         0.14                     
CISPEP   3 ARG A   65    PRO A   66          2        -7.86                     
CISPEP   4 GLY A  116    GLY A  117          2         0.17                     
CISPEP   5 ARG A   65    PRO A   66          3        -9.07                     
CISPEP   6 GLY A  116    GLY A  117          3         0.11                     
CISPEP   7 ARG A   65    PRO A   66          4        -5.77                     
CISPEP   8 GLY A  116    GLY A  117          4         0.25                     
CISPEP   9 ARG A   65    PRO A   66          5        -7.39                     
CISPEP  10 GLY A  116    GLY A  117          5         0.05                     
CISPEP  11 ARG A   65    PRO A   66          6         4.04                     
CISPEP  12 GLY A  116    GLY A  117          6         0.08                     
CISPEP  13 ARG A   65    PRO A   66          7        -8.86                     
CISPEP  14 GLY A  116    GLY A  117          7         0.23                     
CISPEP  15 ARG A   65    PRO A   66          8       -10.52                     
CISPEP  16 GLY A  116    GLY A  117          8         0.17                     
CISPEP  17 ARG A   65    PRO A   66          9        -4.57                     
CISPEP  18 GLY A  116    GLY A  117          9         0.07                     
CISPEP  19 ARG A   65    PRO A   66         10        -9.53                     
CISPEP  20 GLY A  116    GLY A  117         10         0.13                     
CISPEP  21 ARG A   65    PRO A   66         11        -9.57                     
CISPEP  22 GLY A  116    GLY A  117         11         0.13                     
CISPEP  23 ARG A   65    PRO A   66         12        -5.52                     
CISPEP  24 GLY A  116    GLY A  117         12         0.19                     
CISPEP  25 ARG A   65    PRO A   66         13         1.08                     
CISPEP  26 GLY A  116    GLY A  117         13         0.17                     
CISPEP  27 ARG A   65    PRO A   66         14        -3.17                     
CISPEP  28 GLY A  116    GLY A  117         14         0.18                     
CISPEP  29 ARG A   65    PRO A   66         15         5.56                     
CISPEP  30 GLY A  116    GLY A  117         15         0.21                     
CISPEP  31 ARG A   65    PRO A   66         16        -9.08                     
CISPEP  32 GLY A  116    GLY A  117         16         0.08                     
CISPEP  33 ARG A   65    PRO A   66         17        -3.70                     
CISPEP  34 GLY A  116    GLY A  117         17         0.20                     
CISPEP  35 ARG A   65    PRO A   66         18        -5.70                     
CISPEP  36 GLY A  116    GLY A  117         18         0.17                     
CISPEP  37 ARG A   65    PRO A   66         19        -8.59                     
CISPEP  38 GLY A  116    GLY A  117         19         0.14                     
CISPEP  39 ARG A   65    PRO A   66         20       -12.12                     
CISPEP  40 GLY A  116    GLY A  117         20         0.20                     
CISPEP  41 ARG A   65    PRO A   66         21         9.84                     
CISPEP  42 GLY A  116    GLY A  117         21         0.13                     
CISPEP  43 ARG A   65    PRO A   66         22        -3.08                     
CISPEP  44 GLY A  116    GLY A  117         22         0.17                     
CISPEP  45 ARG A   65    PRO A   66         23       -10.81                     
CISPEP  46 GLY A  116    GLY A  117         23         0.20                     
CISPEP  47 ARG A   65    PRO A   66         24       -12.33                     
CISPEP  48 GLY A  116    GLY A  117         24         0.32                     
CISPEP  49 ARG A   65    PRO A   66         25        -9.39                     
CISPEP  50 GLY A  116    GLY A  117         25         0.22                     
SITE     1 AC1 20 ALA A   9  ILE A  16  GLY A  17  LYS A  18                    
SITE     2 AC1 20 GLY A  20  LEU A  22  TRP A  24  GLY A  53                    
SITE     3 AC1 20 LYS A  54  LEU A  75  SER A  76  ARG A  77                    
SITE     4 AC1 20 ARG A  91  SER A  92  LEU A  93  GLY A 117                    
SITE     5 AC1 20 SER A 118  SER A 119  GLU A 123  TRR A 200                    
SITE     1 AC2 11 ILE A   7  VAL A   8  ALA A   9  LEU A  22                    
SITE     2 AC2 11 GLU A  30  PHE A  31  PHE A  34  ILE A  60                    
SITE     3 AC2 11 PRO A  61  VAL A 115  NDP A 190                               
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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