HEADER RNA 15-DEC-04 1WVD TITLE HIV-1 DIS(MAL) DUPLEX COCL2-SOAKED 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, METAL IONS EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,P.WALTER,P.DUMAS REVDAT 3 14-FEB-24 1WVD 1 REMARK LINK REVDAT 2 24-FEB-09 1WVD 1 VERSN REVDAT 1 21-DEC-04 1WVD 0 JRNL AUTH E.ENNIFAR,P.WALTER,P.DUMAS JRNL TITL A CRYSTALLOGRAPHIC STUDY OF THE BINDING OF 13 METAL IONS TO JRNL TITL 2 TWO RELATED RNA DUPLEXES JRNL REF NUCLEIC ACIDS RES. V. 31 2671 2003 JRNL REFN ISSN 0305-1048 JRNL PMID 12736317 JRNL DOI 10.1093/NAR/GKG350 REMARK 2 REMARK 2 RESOLUTION. 2.93 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) : 2.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 673479.450 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 4874 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) : 0.208 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 400 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) : 2.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.10 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 701 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.049 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 : 8 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.61000 REMARK 3 B22 (A**2) : -3.61000 REMARK 3 B33 (A**2) : 7.21000 REMARK 3 B12 (A**2) : 3.27000 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) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.44 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 13.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.580 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 : 0.29 REMARK 3 BSOL : 37.47 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 1WVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000024045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.930 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 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) : 2.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13900 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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): 2.18 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 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.33200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.66400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.66400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.33200 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 U A 3 0.09 SIDE CHAIN REMARK 500 C A 15 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 CO A 503 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 3 O4 REMARK 620 2 G A 4 O6 78.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 507 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 8 OP2 REMARK 620 2 G A 9 N7 93.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 502 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 OP1 REMARK 620 2 G B 9 OP1 157.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 506 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 8 OP2 REMARK 620 2 A B 8 OP2 19.3 REMARK 620 3 G B 9 N7 75.6 94.7 REMARK 620 4 G B 9 N7 55.6 74.8 20.2 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 CO B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y95 RELATED DB: PDB REMARK 900 HIV-1 DIS(MAL) DUPLEX PB-SOAKED REMARK 900 RELATED ID: 1Y6T RELATED DB: PDB REMARK 900 HIV-1 DIS(MAL) DUPLEX CO HEXAMINE-SOAKED REMARK 900 RELATED ID: 1Y6S RELATED DB: PDB REMARK 900 HIV-1 DIS(MAL) DUPLEX BACL2-SOAKED REMARK 900 RELATED ID: 1Y73 RELATED DB: PDB REMARK 900 HIV-1 DIS(MAL) DUPLEX PTCL4-SOAKED REMARK 900 RELATED ID: 1Y90 RELATED DB: PDB REMARK 900 HIV-1 DIS(MAL) DUPLEX MNCL2-SOAKED REMARK 900 RELATED ID: 462D RELATED DB: PDB REMARK 900 HIV-1 DIS(MAL) DUPLEX MG-NATIVE DBREF 1WVD A 1 23 PDB 1WVD 1WVD 1 23 DBREF 1WVD B 1 23 PDB 1WVD 1WVD 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 CO A 501 1 HET CO A 503 1 HET CO A 507 1 HET CO A 508 1 HET CO B 502 1 HET CO B 504 1 HET CO B 505 1 HET CO B 506 1 HETNAM CO COBALT (II) ION FORMUL 3 CO 8(CO 2+) LINK O4 U A 3 CO CO A 503 1555 1555 2.57 LINK O6 G A 4 CO CO A 503 1555 1555 2.67 LINK OP2 A A 8 CO CO A 507 1555 1555 2.35 LINK N7 G A 9 CO CO A 507 1555 1555 2.43 LINK OP1 G A 9 CO CO B 502 1555 1555 2.41 LINK OP2A A B 8 CO CO B 506 1555 1555 2.34 LINK OP2B A B 8 CO CO B 506 1555 1555 2.16 LINK OP1B G B 9 CO CO B 502 1555 1555 2.31 LINK N7 A G B 9 CO CO B 506 1555 1555 2.54 LINK N7 B G B 9 CO CO B 506 1555 1555 2.11 SITE 1 AC1 2 G A 9 G B 9 SITE 1 AC2 2 U A 3 G A 4 SITE 1 AC3 1 G B 7 SITE 1 AC4 2 A B 8 G B 9 SITE 1 AC5 2 A A 8 G A 9 SITE 1 AC6 3 G A 12 G B 12 C B 13 CRYST1 59.168 59.168 63.996 90.00 90.00 120.00 P 31 2 1 12 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 0.016901 0.009758 0.000000 0.00000 SCALE2 0.000000 0.019516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015626 0.00000