PDB Short entry for 1XPF HEADER RNA 08-OCT-04 1XPF TITLE HIV-1 SUBTYPE A GENOMIC RNA DIMERIZATION INITIATION SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP COMPND 3 *GP*CP*AP*AP*G)-3'; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: HIV-1 GENOMIC RNA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA, LOOP-LOOP COMPLEX, HIV-1 EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,P.DUMAS REVDAT 4 13-MAR-24 1XPF 1 REMARK LINK REVDAT 3 24-FEB-09 1XPF 1 VERSN REVDAT 2 07-FEB-06 1XPF 1 JRNL REVDAT 1 18-OCT-05 1XPF 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. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 847446.670 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 7011 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) : 0.243 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.300 REMARK 3 FREE R VALUE TEST SET COUNT : 440 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 945 REMARK 3 BIN R VALUE (WORKING SET) : 0.3920 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 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 : 33 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.86000 REMARK 3 B22 (A**2) : -8.41000 REMARK 3 B33 (A**2) : 6.55000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 15.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.500 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 : 0.34 REMARK 3 BSOL : 66.00 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : SPERMINE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : ION.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : SPERMINE.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030611. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 56.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, AMMONIUM SULFATE, MGCL2, NA REMARK 280 CACODYLATE, SPERMINE, PH 7.0, VAPOR DIFFUSION, HANGING 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 48.98450 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 48.98450 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 14.18200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.10450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 14.18200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.10450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.98450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 14.18200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.10450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.98450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 14.18200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.10450 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 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 NA A 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 1 O2' REMARK 620 2 C A 1 O2 80.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM A 108 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JJM RELATED DB: PDB REMARK 900 RELATED ID: 1JJN RELATED DB: PDB REMARK 900 RELATED ID: 1K9W RELATED DB: PDB REMARK 900 RELATED ID: 1XP7 RELATED DB: PDB REMARK 900 HIV-1 SUBTYPE F REMARK 900 RELATED ID: 1XPE RELATED DB: PDB REMARK 900 HIV-1 SUBTYPE B DBREF 1XPF A 1 23 PDB 1XPF 1XPF 1 23 DBREF 1XPF B 1 23 PDB 1XPF 1XPF 1 23 SEQRES 1 A 23 C U U G C U G A G G U G C SEQRES 2 A 23 A C A C A G C A A G SEQRES 1 B 23 C U U G C U G A G G U G C SEQRES 2 B 23 A C A C A G C A A G HET SO4 A 102 5 HET MG A 104 1 HET NA A 105 1 HET SO4 A 106 5 HET MG A 107 1 HET SPM A 108 14 HET SO4 B 101 5 HET MG B 103 1 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM SPM SPERMINE FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 MG 3(MG 2+) FORMUL 5 NA NA 1+ FORMUL 8 SPM C10 H26 N4 FORMUL 11 HOH *88(H2 O) LINK O2' C A 1 NA NA A 105 1555 1555 2.88 LINK O2 C A 1 NA NA A 105 1555 1555 2.78 LINK OP1 G A 12 MG MG A 107 1555 1555 2.34 SITE 1 AC1 3 HOH A 146 C B 1 HOH B 136 SITE 1 AC2 5 A A 8 G A 9 HOH A 134 HOH A 144 SITE 2 AC2 5 A B 8 SITE 1 AC3 2 C A 1 U A 2 SITE 1 AC4 1 C A 1 SITE 1 AC5 1 G A 12 SITE 1 AC6 8 G A 9 G A 10 U A 11 HOH A 110 SITE 2 AC6 8 HOH A 124 HOH A 138 G B 10 HOH B 119 CRYST1 28.364 120.209 97.969 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 0.035256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010207 0.00000