HEADER RNA 13-DEC-05 2FCX TITLE HIV-1 DIS KISSING-LOOP IN COMPLEX WITH NEAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 DIS RNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SUBTYPE F HIV-1 KEYWDS HIV-1, RNA, AMINOGLYCOSIDE, ANTIBIOTICS EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,J.C.PAILLART,R.MARQUET,P.DUMAS REVDAT 4 14-FEB-24 2FCX 1 HETSYN REVDAT 3 29-JUL-20 2FCX 1 COMPND REMARK HETNAM HETSYN REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 24-FEB-09 2FCX 1 VERSN REVDAT 1 16-MAY-06 2FCX 0 JRNL AUTH E.ENNIFAR,J.C.PAILLART,A.BODLENNER,P.WALTER,J.-M.WEIBEL, JRNL AUTH 2 A.-M.AUBERTIN,P.PALE,P.DUMAS,R.MARQUET JRNL TITL TARGETING THE DIMERIZATION INITIATION SITE OF HIV-1 RNA WITH JRNL TITL 2 AMINOGLYCOSIDES: FROM CRYSTAL TO CELL. JRNL REF NUCLEIC ACIDS RES. V. 34 2328 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16679451 JRNL DOI 10.1093/NAR/GKL317 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 791329.060 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18818 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) : 0.267 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1457 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2768 REMARK 3 BIN R VALUE (WORKING SET) : 0.4120 REMARK 3 BIN FREE R VALUE : 0.4190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 248 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 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 : 48 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -15.26000 REMARK 3 B33 (A**2) : 15.44000 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) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.48 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) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.52 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 12.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 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 : 0.39 REMARK 3 BSOL : 43.94 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 : NEAMINE.PARAM REMARK 3 PARAMETER FILE 6 : 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 : BRU.TOP REMARK 3 TOPOLOGY FILE 5 : NEAMINE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000035728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-04; 01-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SLS; ESRF REMARK 200 BEAMLINE : X06SA; ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.91961; 0.91950, 0.91965, REMARK 200 0.91640 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARMOSAIC 225 MM REMARK 200 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18852 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 49.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, KCL, MGCL2, NA CACODYLATE, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, 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 47.51900 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 47.51900 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 13.50250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.69750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 13.50250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.69750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.51900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 13.50250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.69750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.51900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 13.50250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.69750 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 0.06 SIDE CHAIN 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 K A 24 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 5BU A 3 O4 REMARK 620 2 G A 4 O6 74.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 25 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 8 OP1 REMARK 620 2 A A 9 OP2 95.3 REMARK 620 3 XXX A 101 O4 82.0 124.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 24 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 5BU B 3 O4 REMARK 620 2 G B 4 O6 94.0 REMARK 620 3 HOH B 217 O 57.5 104.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XP7 RELATED DB: PDB REMARK 900 SUBTYPE F HIV-1 DIS KISSING-LOOP REMARK 900 RELATED ID: 1Y3S RELATED DB: PDB REMARK 900 SUBTYPE F HIV-1 DIS KISSING-LOOP REMARK 900 RELATED ID: 2FCY RELATED DB: PDB REMARK 900 HIV-1 DIS KISSING-LOOP IN COMPLEX WITH NEOMYCIN REMARK 900 RELATED ID: 2FCZ RELATED DB: PDB REMARK 900 HIV-1 DIS KISSING-LOOP IN COMPLEX WITH RIBOSTAMYCIN REMARK 900 RELATED ID: 2FD0 RELATED DB: PDB REMARK 900 HIV-1 DIS KISSING-LOOP IN COMPLEX WITH LIVIDOMYCIN DBREF 2FCX A 1 23 PDB 2FCX 2FCX 1 23 DBREF 2FCX B 1 23 PDB 2FCX 2FCX 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 2FCX 5BU A 3 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 2FCX 5BU B 3 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE HET 5BU A 3 21 HET 5BU B 3 21 HET K A 24 1 HET K A 25 1 HET CL A 26 1 HET XXX A 101 22 HET K B 24 1 HET XXX B 201 22 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM XXX (1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL 2, HETNAM 2 XXX 6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE HETSYN XXX (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3- HETSYN 2 XXX DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)- HETSYN 3 XXX TETRAHYDRO-2H-PYRA N-3,4-DIOL; NEOMYCIN A; NEAMINE; HETSYN 4 XXX (1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL HETSYN 5 XXX 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOSIDE; (1R,2R,3S, HETSYN 6 XXX 4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL 2,6- HETSYN 7 XXX DIAMINO-2,6-DIDEOXY-D-GLUCOSIDE; (1R,2R,3S,4R,6S)-4,6- HETSYN 8 XXX DIAMINO-2,3-DIHYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6- HETSYN 9 XXX DIDEOXY-GLUCOSIDE FORMUL 1 5BU 2(C9 H12 BR N2 O9 P) FORMUL 3 K 3(K 1+) FORMUL 5 CL CL 1- FORMUL 6 XXX 2(C12 H26 N4 O6) FORMUL 9 HOH *35(H2 O) LINK O3' U A 2 P 5BU A 3 1555 1555 1.62 LINK O3' 5BU A 3 P G A 4 1555 1555 1.61 LINK O3' U B 2 P 5BU B 3 1555 1555 1.61 LINK O3' 5BU B 3 P G B 4 1555 1555 1.61 LINK O4 5BU A 3 K K A 24 1555 1555 2.88 LINK O6 G A 4 K K A 24 1555 1555 2.73 LINK OP1 A A 8 K K A 25 1555 1555 2.43 LINK OP2 A A 9 K K A 25 1555 1555 2.87 LINK K K A 25 O4 XXX A 101 1555 1555 3.02 LINK O4 5BU B 3 K K B 24 1555 1555 2.72 LINK O6 G B 4 K K B 24 1555 1555 2.42 LINK K K B 24 O HOH B 217 1555 1555 3.28 CRYST1 27.005 113.395 95.038 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 0.037030 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010522 0.00000