PDB Short entry for 1YUI
HEADER    DNA BINDING PROTEIN/DNA                 31-DEC-96   1YUI              
TITLE     SOLUTION NMR STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX,                
TITLE    2 REGULARIZED MEAN STRUCTURE                                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3');           
COMPND   3 CHAIN: B;                                                            
COMPND   4 ENGINEERED: YES;                                                     
COMPND   5 MOL_ID: 2;                                                           
COMPND   6 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3');           
COMPND   7 CHAIN: C;                                                            
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 MOL_ID: 3;                                                           
COMPND  10 MOLECULE: GAGA-FACTOR;                                               
COMPND  11 CHAIN: A;                                                            
COMPND  12 FRAGMENT: DNA BINDING DOMAIN, RESIDUES 310 - 372                     
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 MOL_ID: 2;                                                           
SOURCE   4 SYNTHETIC: YES;                                                      
SOURCE   5 MOL_ID: 3;                                                           
SOURCE   6 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER;                        
SOURCE   7 ORGANISM_COMMON: FRUIT FLY;                                          
SOURCE   8 ORGANISM_TAXID: 7227                                                 
KEYWDS    COMPLEX (DNA-BINDING PROTEIN/DNA), CHROMATIN REMODELING,              
KEYWDS   2 DNA BINDING PROTEIN/DNA COMPLEX                                      
EXPDTA    SOLUTION NMR                                                          
AUTHOR    G.M.CLORE,J.G.OMICHINSKI,A.M.GRONENBORN                               
REVDAT   2   24-FEB-09 1YUI    1       VERSN                                    
REVDAT   1   31-DEC-97 1YUI    0                                                
JRNL        AUTH   J.G.OMICHINSKI,P.V.PEDONE,G.FELSENFELD,                      
JRNL        AUTH 2 A.M.GRONENBORN,G.M.CLORE                                     
JRNL        TITL   THE SOLUTION STRUCTURE OF A SPECIFIC GAGA                    
JRNL        TITL 2 FACTOR-DNA COMPLEX REVEALS A MODULAR BINDING MODE.           
JRNL        REF    NAT.STRUCT.BIOL.              V.   4   122 1997              
JRNL        REFN                   ISSN 1072-8368                               
JRNL        PMID   9033593                                                      
JRNL        DOI    10.1038/NSB0297-122                                          
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR (SEE ABOVE)                                   
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS:                                           
REMARK   3  THE 3D STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX WAS SOLVED          
REMARK   3  BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED             
REMARK   3  NMR AND IS BASED ON 1475 EXPERIMENTAL NMR RESTRAINTS:               
REMARK   3  (A) INTRAPROTEIN: 188 SEQUENTIAL (|I- J|=1), 134 MEDIUM             
REMARK   3  RANGE (1 < |I-J| <=5) AND 95 LONG RANGE (|I-J| >5)                  
REMARK   3  INTERRESIDUES AND 275 INTRARESIDUE APPROXIMATE INTERPROTON          
REMARK   3  DISTANCE RESTRAINTS; 140 TORSION ANGLE RESTRAINTS; 33               
REMARK   3  THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 94               
REMARK   3  (48 CALPHA AND 46 CBETA) 13C SHIFT RESTRAINTS.  (NUMBERS            
REMARK   3  OF RESIDUES 10 - 61)                                                
REMARK   3  (B) INTRA-DNA: 124 INTRARESIDUE, 112 SEQUENTIAL                     
REMARK   3  INTRASTRAND, 21 INTERSTRAND INTERPROTON DISTANCE                    
REMARK   3  RESTRAINTS; 102 TORSION ANGLE RESTRAINTS (FOR ALPHA, BETA,          
REMARK   3  GAMMA, DELTA, EPSILON AND AND ZETA BACKBONE TORSION                 
REMARK   3  ANGLES).                                                            
REMARK   3  (C) INTERMOLECULAR: 75 INTERPROTON DISTANCE RESTRAINTS.             
REMARK   3  THE EXPERIMENTAL NMR RESTRAINTS ARE SUPPLEMENTED BY                 
REMARK   3  HYDROGEN BONDING RESTRAINTS: 24 DISTANCES FOR 12 BACKBONE           
REMARK   3  HYDROGEN BONDS WITHIN THE PROTEIN, 58 DISTANCES FOR                 
REMARK   3  WATSON-CRICK BASE-PAIRING WITHIN THE DNA, AND 10 AMBIGUOUS          
REMARK   3  DISTANCE RESTRAINTS BETWEEN THE PROTEIN AND THE DNA.  THE           
REMARK   3  RESTRAINTS HAVE BEEN DEPOSITED.                                     
REMARK   3                                                                      
REMARK   3  THE STRUCTURES WERE CALCULATED USING THE SIMULATED                  
REMARK   3  ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229,          
REMARK   3  129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED             
REMARK   3  TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J.          
REMARK   3  MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL              
REMARK   3  SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B             
REMARK   3  106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE               
REMARK   3  POTENTIAL (KUSZEWSKI ET AL.(1996) PROTEIN SCI. 5, 1067-1080         
REMARK   3                                                                      
REMARK   3  THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN           
REMARK   3  THIS ENTRY AND 50 STRUCTURES ARE PRESENTED IN ENTRY 1YUJ.           
REMARK   3  IN THE RESTRAINED REGULARIZED MEAN COORDINATES THE LAST             
REMARK   3  COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE            
REMARK   3  INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN              
REMARK   3  COORDINATE POSITIONS.  THE LAST COLUMN IN THE INDIVIDUAL SA         
REMARK   3  STRUCTURES HAS NO MEANING.  BEST FITTING TO GENERATE THE            
REMARK   3  AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 14 - 58 OF            
REMARK   3  THE PROTEIN AND BASE PAIRS 1 - 11 OF THE DNA (RESIDUES 10 -         
REMARK   3  13 AND 59 - 61 ARE DISORDERED IN SOLUTION).  RESIDUE 10             
REMARK   3  CORRESPONDS TO RESIDUE 319 OF THE NATURAL SEQUENCE.  NOTE           
REMARK   3  THE OCCUPANCY FIELD HAS NO MEANING.                                 
REMARK   4                                                                      
REMARK   4 1YUI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 303.50                             
REMARK 210  PH                             : 6.00                               
REMARK 210  IONIC STRENGTH                 : NULL                               
REMARK 210  PRESSURE                       : NULL                               
REMARK 210  SAMPLE CONTENTS                : NULL                               
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : TRIPLE RESONANCE                   
REMARK 210  SPECTROMETER FIELD STRENGTH    : 500 MHZ, 600 MHZ                   
REMARK 210  SPECTROMETER MODEL             : AMX500, AMX600                     
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : X-PLOR (SEE ABOVE)                 
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : NULL                               
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 1                                  
REMARK 210 CONFORMERS, SELECTION CRITERIA  : REGULARIZED MEAN STRUCTURE         
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL                
REMARK 210                                                                      
REMARK 210 REMARK: TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN 12C-              
REMARK 210  FILTERED NOE, 12C-FILTERED HOHAHA AND 1H-1H NOE FOR DNA.            
REMARK 210  QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS 3D 15N-           
REMARK 210  SEPARATED, 3D 13C-SEPARATED, 3D 12C-FILTERED 3D 13C-                
REMARK 210  SEPARATED/12C-FILTERED, AND 2D 1H-1H NOE EXPERIMENTS.               
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: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500     DG B 101   O4' -  C1' -  N9  ANGL. DEV. =   2.1 DEGREES          
REMARK 500     DC B 102   O4' -  C1' -  N1  ANGL. DEV. =   2.1 DEGREES          
REMARK 500     DC B 103   O4' -  C1' -  N1  ANGL. DEV. =   2.3 DEGREES          
REMARK 500     DG B 104   O4' -  C1' -  N9  ANGL. DEV. =   2.5 DEGREES          
REMARK 500     DA B 105   O4' -  C1' -  N9  ANGL. DEV. =   3.1 DEGREES          
REMARK 500     DG B 106   O4' -  C1' -  N9  ANGL. DEV. =   2.3 DEGREES          
REMARK 500     DA B 107   O4' -  C1' -  N9  ANGL. DEV. =   2.3 DEGREES          
REMARK 500     DG B 108   O4' -  C1' -  N9  ANGL. DEV. =   3.1 DEGREES          
REMARK 500     DT B 109   O4' -  C1' -  N1  ANGL. DEV. =   2.1 DEGREES          
REMARK 500     DA B 110   O4' -  C1' -  N9  ANGL. DEV. =   2.2 DEGREES          
REMARK 500     DC B 111   O4' -  C1' -  N1  ANGL. DEV. =   2.6 DEGREES          
REMARK 500     DG C 112   O4' -  C1' -  N9  ANGL. DEV. =   2.5 DEGREES          
REMARK 500     DT C 113   O4' -  C1' -  N1  ANGL. DEV. =   2.2 DEGREES          
REMARK 500     DT C 113   C6  -  C5  -  C7  ANGL. DEV. =  -3.7 DEGREES          
REMARK 500     DA C 114   O4' -  C1' -  N9  ANGL. DEV. =   2.6 DEGREES          
REMARK 500     DC C 115   O4' -  C1' -  N1  ANGL. DEV. =   1.8 DEGREES          
REMARK 500     DT C 116   O4' -  C1' -  N1  ANGL. DEV. =   1.9 DEGREES          
REMARK 500     DC C 117   O4' -  C1' -  N1  ANGL. DEV. =   3.1 DEGREES          
REMARK 500     DT C 118   O4' -  C1' -  N1  ANGL. DEV. =   3.3 DEGREES          
REMARK 500     DC C 119   O4' -  C1' -  N1  ANGL. DEV. =   2.4 DEGREES          
REMARK 500     DG C 120   O4' -  C1' -  N9  ANGL. DEV. =   2.7 DEGREES          
REMARK 500     DG C 121   O4' -  C1' -  N9  ANGL. DEV. =   2.3 DEGREES          
REMARK 500     DC C 122   O4' -  C1' -  N1  ANGL. DEV. =   2.0 DEGREES          
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    ALA A  12       76.32   -159.26                                   
REMARK 500    LYS A  23       76.45   -104.38                                   
REMARK 500    PRO A  33      152.93    -37.70                                   
REMARK 500    TYR A  40       17.58     52.98                                   
REMARK 500    HIS A  57      -73.20   -152.68                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;              
REMARK 620  SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                            
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              ZN A  64  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A  36   SG                                                     
REMARK 620 2 CYS A  39   SG  107.3                                              
REMARK 620 3 HIS A  52   NE2 106.2 107.5                                        
REMARK 620 4 HIS A  57   NE2 107.3 121.4 106.3                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 64                   
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1YUJ   RELATED DB: PDB                                   
REMARK 900 ENSEMBLE OF 50 STRUCTURES                                            
DBREF  1YUI A   10    63  UNP    Q08605   GAGA_DROME     319    372             
DBREF  1YUI B  101   111  PDB    1YUI     1YUI           101    111             
DBREF  1YUI C  112   122  PDB    1YUI     1YUI           112    122             
SEQRES   1 B   11   DG  DC  DC  DG  DA  DG  DA  DG  DT  DA  DC                  
SEQRES   1 C   11   DG  DT  DA  DC  DT  DC  DT  DC  DG  DG  DC                  
SEQRES   1 A   54  PRO LYS ALA LYS ARG ALA LYS HIS PRO PRO GLY THR GLU          
SEQRES   2 A   54  LYS PRO ARG SER ARG SER GLN SER GLU GLN PRO ALA THR          
SEQRES   3 A   54  CYS PRO ILE CYS TYR ALA VAL ILE ARG GLN SER ARG ASN          
SEQRES   4 A   54  LEU ARG ARG HIS LEU GLU LEU ARG HIS PHE ALA LYS PRO          
SEQRES   5 A   54  GLY VAL                                                      
HET     ZN  A  64       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   4   ZN    ZN 2+                                                        
HELIX    1   1 ARG A   25  SER A   28  1                                   4    
HELIX    2   2 SER A   46  ARG A   56  1                                  11    
SHEET    1   A 2 ALA A  34  THR A  35  0                                        
SHEET    2   A 2 VAL A  42  ILE A  43 -1  N  ILE A  43   O  ALA A  34           
LINK        ZN    ZN A  64                 SG  CYS A  36     1555   1555  2.30  
LINK        ZN    ZN A  64                 SG  CYS A  39     1555   1555  2.31  
LINK        ZN    ZN A  64                 NE2 HIS A  52     1555   1555  2.00  
LINK        ZN    ZN A  64                 NE2 HIS A  57     1555   1555  2.01  
SITE     1 AC1  4 CYS A  36  CYS A  39  HIS A  52  HIS A  57                    
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