HEADER    RNA                                     22-FEB-05   1YXP              
TITLE     HIV-1 DIS RNA SUBTYPE F- ZN SOAKED                                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-R(*CP*UP*(5BU)                                          
COMPND   3 P*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3';    
COMPND   4 CHAIN: A, B;                                                         
COMPND   5 SYNONYM: HIV-1 GENOMIC RNA DIS;                                      
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    HIV-1, RNA, KISSING-LOOP, METAL IONS                                  
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    E.ENNIFAR,P.DUMAS                                                     
REVDAT   3   14-FEB-24 1YXP    1       REMARK LINK                              
REVDAT   2   24-FEB-09 1YXP    1       VERSN                                    
REVDAT   1   31-JAN-06 1YXP    0                                                
JRNL        AUTH   E.ENNIFAR,P.DUMAS                                            
JRNL        TITL   POLYMORPHISM OF BULGED-OUT RESIDUES IN HIV-1 RNA DIS KISSING 
JRNL        TITL 2 COMPLEX AND STRUCTURE COMPARISON WITH SOLUTION STUDIES.      
JRNL        REF    J.MOL.BIOL.                   V. 356   771 2006              
JRNL        REFN                   ISSN 0022-2836                               
JRNL        PMID   16403527                                                     
JRNL        DOI    10.1016/J.JMB.2005.12.022                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.40 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS 1.1                                              
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : NULL                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 7.98                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 589191.020                     
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 91.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 10089                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.270                           
REMARK   3   FREE R VALUE                     : 0.303                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 1006                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.010                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 6                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.40                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.55                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 82.10                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1381                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.4360                       
REMARK   3   BIN FREE R VALUE                    : 0.4330                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 9.00                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 137                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.037                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 0                                       
REMARK   3   NUCLEIC ACID ATOMS       : 980                                     
REMARK   3   HETEROGEN ATOMS          : 2                                       
REMARK   3   SOLVENT ATOMS            : 0                                       
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 70.70                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 50.00                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 2.20000                                              
REMARK   3    B22 (A**2) : -21.07000                                            
REMARK   3    B33 (A**2) : 18.87000                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.48                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.68                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.53                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.71                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.006                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.000                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 15.20                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.380                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.36                                                 
REMARK   3   BSOL        : 35.88                                                
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : WATER_REP.PARAM                                
REMARK   3  PARAMETER FILE  2  : DNA-RNA.PARAM                                  
REMARK   3  PARAMETER FILE  3  : ION.PARAM                                      
REMARK   3  PARAMETER FILE  4  : BRU_REP.PARAM                                  
REMARK   3  PARAMETER FILE  5  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : WATER.TOP                                      
REMARK   3  TOPOLOGY FILE  2   : DNA-RNA.TOP                                    
REMARK   3  TOPOLOGY FILE  3   : ION.TOP                                        
REMARK   3  TOPOLOGY FILE  4   : NULL                                           
REMARK   3  TOPOLOGY FILE  5   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1YXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-05.                  
REMARK 100 THE DEPOSITION ID IS D_1000032043.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 13-DEC-04                          
REMARK 200  TEMPERATURE           (KELVIN) : 120                                
REMARK 200  PH                             : 7.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X06SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.28238                            
REMARK 200  MONOCHROMATOR                  : CRYSTAL                            
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10685                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.400                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.4                               
REMARK 200  DATA REDUNDANCY                : 2.200                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.05600                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 15.2000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.55                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 97.5                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.21400                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 3.200                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS            
REMARK 200 SOFTWARE USED: CNS                                                   
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 50.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, AMMONIUM SULFATE, MGCL2, NA     
REMARK 280  CACODYLATE, SPERMINE, PH 7.0, VAPOR DIFFUSION, SITTING DROP,        
REMARK 280  TEMPERATURE 310K                                                    
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -X,Y,-Z+1/2                                             
REMARK 290       4555   X,-Y,-Z                                                 
REMARK 290       5555   X+1/2,Y+1/2,Z                                           
REMARK 290       6555   -X+1/2,-Y+1/2,Z+1/2                                     
REMARK 290       7555   -X+1/2,Y+1/2,-Z+1/2                                     
REMARK 290       8555   X+1/2,-Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       46.66700            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       46.66700            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000       13.63750            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       59.31450            
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       13.63750            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       59.31450            
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       46.66700            
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       13.63750            
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       59.31450            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       46.66700            
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       13.63750            
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       59.31450            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
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: DIMERIC                           
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B                                  
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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500      A A   9         0.05    SIDE CHAIN                              
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 ZN A 100                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 101                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1Y3S   RELATED DB: PDB                                   
REMARK 900 HIV-1 DIS RNA SUBTYPE F - MPD FORM                                   
REMARK 900 RELATED ID: 1Y3O   RELATED DB: PDB                                   
REMARK 900 HIV-1 DIS RNA SUBTYPE F- MN SOAKED                                   
REMARK 900 RELATED ID: 1XP7   RELATED DB: PDB                                   
REMARK 900 HIV-1 SUBTYPE F GENOMIC RNA DIMERIZATION INITIATION SITE - PEG FORM  
DBREF  1YXP A    1    23  PDB    1YXP     1YXP             1     23             
DBREF  1YXP B    1    23  PDB    1YXP     1YXP             1     23             
SEQRES   1 A   23    C   U 5BU   G   C   U   G   A   A   G   U   G   C          
SEQRES   2 A   23    A   C   A   C   A   G   C   A   A   G                      
SEQRES   1 B   23    C   U 5BU   G   C   U   G   A   A   G   U   G   C          
SEQRES   2 B   23    A   C   A   C   A   G   C   A   A   G                      
MODRES 1YXP 5BU A    3    U  5-BROMO-URIDINE-5'-MONOPHOSPHATE                   
MODRES 1YXP 5BU B    3    U  5-BROMO-URIDINE-5'-MONOPHOSPHATE                   
HET    5BU  A   3      21                                                       
HET    5BU  B   3      21                                                       
HET     ZN  A 100       1                                                       
HET     ZN  B 101       1                                                       
HETNAM     5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE                                 
HETNAM      ZN ZINC ION                                                         
FORMUL   1  5BU    2(C9 H12 BR N2 O9 P)                                         
FORMUL   3   ZN    2(ZN 2+)                                                     
LINK         O3'   U A   2                 P   5BU A   3     1555   1555  1.61  
LINK         O3' 5BU A   3                 P     G A   4     1555   1555  1.62  
LINK         O3'   U B   2                 P   5BU B   3     1555   1555  1.60  
LINK         O3' 5BU B   3                 P     G B   4     1555   1555  1.60  
LINK         N7    G A  10                ZN    ZN A 100     1555   1555  2.35  
LINK         N7    G B  10                ZN    ZN B 101     1555   1555  2.26  
SITE     1 AC1  1   G A  10                                                     
SITE     1 AC2  1   G B  10                                                     
CRYST1   27.275  118.629   93.334  90.00  90.00  90.00 C 2 2 21     16          
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      0.036664  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.008430  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.010714        0.00000