HEADER RNA 15-DEC-04 1Y99 TITLE HIV-1 SUBTYPE A DIS RNA DUPLEX 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 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HIV-1 DIS RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS HIV-1, RNA, BULGE, MAGNESIUM EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,M.YUSUPOV,P.WALTER,R.MARQUET,B.EHRESMANN,C.EHRESMANN, AUTHOR 2 P.DUMAS REVDAT 3 23-AUG-23 1Y99 1 REMARK LINK REVDAT 2 24-FEB-09 1Y99 1 VERSN REVDAT 1 21-DEC-04 1Y99 0 JRNL AUTH E.ENNIFAR,M.YUSUPOV,P.WALTER,R.MARQUET,B.EHRESMANN, JRNL AUTH 2 C.EHRESMANN,P.DUMAS JRNL TITL THE CRYSTAL STRUCTURE OF THE DIMERIZATION INITIATION SITE OF JRNL TITL 2 GENOMIC HIV-1 RNA REVEALS AN EXTENDED DUPLEX WITH TWO JRNL TITL 3 ADENINE BULGES JRNL REF STRUCTURE FOLD.DES. V. 7 1439 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10574792 JRNL DOI 10.1016/S0969-2126(00)80033-7 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) : 9.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 605002.230 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 5001 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) : 0.225 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 519 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) (%) : 85.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 653 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE : 0.4640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.053 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 : 7 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.13000 REMARK 3 B22 (A**2) : 13.52000 REMARK 3 B33 (A**2) : -5.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.63000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.45 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 10.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230 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) : 2.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.150 ; 2.000 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 : 0.29 REMARK 3 BSOL : 29.84 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 1Y99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9615 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 6534 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35100 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 462D 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): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SPERMINE, KCL, MGCL2, NA REMARK 280 CACODYLATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 127 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 169 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 176 LIES ON A SPECIAL POSITION. 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 MG A 720 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 4 O6 REMARK 620 2 HOH A 128 O 127.6 REMARK 620 3 C B 20 N4 68.2 163.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 760 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 8 OP2 REMARK 620 2 A A 8 OP2 16.2 REMARK 620 3 G A 9 N7 81.9 96.1 REMARK 620 4 G A 9 N7 86.7 101.0 5.0 REMARK 620 5 HOH A 122 O 104.6 110.1 98.9 96.4 REMARK 620 6 HOH A 761 O 81.3 65.6 157.4 161.7 100.0 REMARK 620 7 HOH A 762 O 79.9 75.0 78.6 80.7 174.6 83.5 REMARK 620 8 HOH A 763 O 155.9 151.4 85.8 81.8 97.8 103.8 77.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 750 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 OP1 REMARK 620 2 G B 9 OP1 101.8 REMARK 620 3 G B 10 OP2 137.3 71.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 710 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 12 O6 REMARK 620 2 HOH A 167 O 85.1 REMARK 620 3 HOH A 172 O 70.1 79.5 REMARK 620 4 HOH B 145 O 136.3 102.2 153.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 730 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 129 O REMARK 620 2 HOH A 149 O 125.3 REMARK 620 3 G B 4 O6 90.3 99.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 720 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 730 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 750 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 760 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 462D RELATED DB: PDB REMARK 900 HIV-1 SUBTYPE A DIS RNA DUPLEX REMARK 900 RELATED ID: 1JJN RELATED DB: PDB REMARK 900 HIV-1 SUBTYPE A DIS RNA KISSING-COMPLEX REMARK 900 RELATED ID: 1K9W RELATED DB: PDB REMARK 900 HIV-1 SUBTYPE A DIS RNA KISSING-COMPLEX DBREF 1Y99 A 1 23 PDB 1Y99 1Y99 1 23 DBREF 1Y99 B 1 23 PDB 1Y99 1Y99 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 MG A 700 1 HET MG A 710 1 HET MG A 720 1 HET MG A 760 1 HET MG B 730 1 HET MG B 740 1 HET MG B 750 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 7(MG 2+) FORMUL 10 HOH *82(H2 O) LINK O6 G A 4 MG MG A 720 1555 1555 2.46 LINK OP2B A A 8 MG MG A 760 1555 1555 2.36 LINK OP2A A A 8 MG MG A 760 1555 1555 2.47 LINK N7 B G A 9 MG MG A 760 1555 1555 2.58 LINK N7 A G A 9 MG MG A 760 1555 1555 2.58 LINK OP1A G A 9 MG MG B 750 1555 1555 2.87 LINK O6 G A 12 MG MG A 710 1555 1555 3.06 LINK O HOH A 122 MG MG A 760 1555 1555 2.07 LINK O HOH A 128 MG MG A 720 1555 1555 2.43 LINK O HOH A 129 MG MG B 730 1555 1555 2.74 LINK O HOH A 149 MG MG B 730 1555 1555 2.63 LINK O HOH A 167 MG MG A 710 1555 1555 2.55 LINK O HOH A 172 MG MG A 710 1555 1555 2.95 LINK MG MG A 710 O HOH B 145 1555 1555 2.98 LINK MG MG A 720 N4 C B 20 1555 1555 3.03 LINK MG MG A 760 O HOH A 761 1555 1555 2.14 LINK MG MG A 760 O HOH A 762 1555 1555 2.12 LINK MG MG A 760 O HOH A 763 1555 1555 2.34 LINK O6 G B 4 MG MG B 730 1555 1555 2.94 LINK OP1 G B 9 MG MG B 750 1555 1555 2.74 LINK OP2 G B 10 MG MG B 750 1555 1555 3.14 SITE 1 AC1 4 G A 12 HOH A 167 HOH A 172 HOH B 145 SITE 1 AC2 5 U A 3 G A 4 HOH A 128 G B 19 SITE 2 AC2 5 C B 20 SITE 1 AC3 4 HOH A 129 HOH A 149 U B 3 G B 4 SITE 1 AC4 3 G A 9 G B 9 G B 10 SITE 1 AC5 6 A A 8 G A 9 HOH A 122 HOH A 761 SITE 2 AC5 6 HOH A 762 HOH A 763 CRYST1 45.698 31.422 51.188 90.00 115.82 90.00 P 1 2 1 4 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 0.021883 0.000000 0.010588 0.00000 SCALE2 0.000000 0.031825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021702 0.00000