HEADER RNA 21-JUL-08 3DVV TITLE CRYSTAL STRUCTURE OF HIV-1 SUBTYPE F DIS EXTENDED DUPLEX RNA BOUND TO TITLE 2 RIBOSTAMYCIN (U267OME) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 GENOMIC RNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS HIV-1, RNA, ANTIBIOTIC, AMINOGLYCOSIDE EXPDTA X-RAY DIFFRACTION AUTHOR E.ENNIFAR,P.DUMAS,V.OLIERIC REVDAT 3 01-NOV-23 3DVV 1 REMARK HETSYN LINK REVDAT 2 24-FEB-09 3DVV 1 VERSN REVDAT 1 12-AUG-08 3DVV 0 JRNL AUTH V.OLIERIC,U.RIEDER,K.LANG,A.SERGANOV,C.SCHULZE-BRISE, JRNL AUTH 2 R.MICURA,P.DUMAS,E.ENNIFAR JRNL TITL A FAST STRATEGY FOR SELENIUM DERIVATIZATION AND PHASING OF JRNL TITL 2 RNA STRUCTURES JRNL REF TO BE PUBLISHED JRNL REFN 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) : 18.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 741857.930 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 9635 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) : 0.268 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT : 795 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1488 REMARK 3 BIN R VALUE (WORKING SET) : 0.4250 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 121 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 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 : 67 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.14000 REMARK 3 B22 (A**2) : 14.78000 REMARK 3 B33 (A**2) : -12.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM SIGMAA (A) : 0.40 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) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 12.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 5.590 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 : 36.98 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 : LUC.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : OMU_XPLOR.PARAM REMARK 3 PARAMETER FILE 5 : RIBOSTAMYCINE.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 : OMU_XPLOR.TOP REMARK 3 TOPOLOGY FILE 5 : RIBOSTAMYCINE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9829 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 29.0000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30900 REMARK 200 FOR SHELL : 9.800 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: PDB ID 3C3Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, CACODYLATE, MGCL2, KCL, PH 6.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.85150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.24450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.85150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.24450 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 A A 8 C2' - C3' - O3' ANGL. DEV. = 13.2 DEGREES 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 25 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OMU A 3 O4 REMARK 620 2 G A 4 O6 74.0 REMARK 620 N 1 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 G A 10 OP1 REMARK 620 2 A B 8 O2' 103.3 REMARK 620 3 HOH B 42 O 90.4 67.5 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 OMU B 3 O4 REMARK 620 2 G B 4 O6 72.8 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 K A 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RIO A 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RIO B 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C3Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HIV-1 SUBTYPE F DIS EXTENDED DUPLEX RNA BOUND REMARK 900 TO RIBOSTAMYCIN (U267SEME) DBREF 3DVV A 1 23 PDB 3DVV 3DVV 1 23 DBREF 3DVV B 1 23 PDB 3DVV 3DVV 1 23 SEQRES 1 A 23 C U OMU 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 OMU 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 3DVV OMU A 3 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 3DVV OMU B 3 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET OMU A 3 21 HET OMU B 3 21 HET K A 24 1 HET K A 25 1 HET CL A 26 1 HET RIO A 27 31 HET K B 24 1 HET K B 25 1 HET RIO B 26 31 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM RIO RIBOSTAMYCIN HETSYN RIO 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY- HETSYN 2 RIO 5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY- HETSYN 3 RIO CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL; (1R,2R,3S, HETSYN 4 RIO 4R,6S)-4,6-DIAMINO-3-HYDROXY-2-(BETA-D- HETSYN 5 RIO RIBOFURANOSYLOXY)CYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY- HETSYN 6 RIO ALPHA-D-GLUCOPYRANOSIDE FORMUL 1 OMU 2(C10 H15 N2 O9 P) FORMUL 3 K 4(K 1+) FORMUL 5 CL CL 1- FORMUL 6 RIO 2(C17 H34 N4 O10) FORMUL 10 HOH *44(H2 O) LINK O3' U A 2 P OMU A 3 1555 1555 1.61 LINK O3' OMU A 3 P G A 4 1555 1555 1.61 LINK O3' U B 2 P OMU B 3 1555 1555 1.61 LINK O3' OMU B 3 P G B 4 1555 1555 1.60 LINK O4 OMU A 3 K K A 25 1555 1555 2.77 LINK O6 G A 4 K K A 25 1555 1555 2.58 LINK OP1 G A 10 K K A 24 1555 1555 2.77 LINK K K A 24 O2' A B 8 1555 1555 2.76 LINK K K A 24 O HOH B 42 1555 1555 2.36 LINK O2' U B 2 K K B 25 1555 1555 2.99 LINK O4 OMU B 3 K K B 24 1555 1555 2.83 LINK O6 G B 4 K K B 24 1555 1555 2.99 SITE 1 AC1 4 A A 9 G A 10 A B 8 HOH B 42 SITE 1 AC2 2 OMU A 3 G A 4 SITE 1 AC3 1 C A 17 SITE 1 AC4 2 OMU B 3 G B 4 SITE 1 AC5 2 U B 2 C B 13 SITE 1 AC6 15 G A 7 A A 8 A A 9 G A 10 SITE 2 AC6 15 U A 11 HOH A 30 HOH A 33 HOH A 36 SITE 3 AC6 15 HOH A 37 HOH A 45 HOH A 50 A B 14 SITE 4 AC6 15 C B 15 A B 16 HOH B 27 SITE 1 AC7 14 C A 13 A A 14 C A 15 A A 16 SITE 2 AC7 14 HOH A 45 G B 7 A B 8 A B 9 SITE 3 AC7 14 G B 10 U B 11 G B 12 HOH B 28 SITE 4 AC7 14 HOH B 31 HOH B 38 CRYST1 99.703 30.489 58.004 90.00 122.25 90.00 C 1 2 1 8 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 0.010030 0.000000 0.006330 0.00000 SCALE2 0.000000 0.032799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020386 0.00000