10 20 30 40 50 60 70 80 3C44 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 29-JAN-08 3C44
TITLE CRYSTAL STRUCTURE OF HIV-1 SUBTYPE F DIS EXTENDED DUPLEX TITLE 2 RNA BOUND TO PAROMOMYCIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 SUBTYPE F GENOMIC RNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS HIV-1, RNA, ANTIBIOTIC, PAROMOMYCIN, EXTENDED DUPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.FREISZ,E.ENNIFAR,P.DUMAS
REVDAT 2 24-FEB-09 3C44 1 VERSN REVDAT 1 06-MAY-08 3C44 0
JRNL AUTH S.FREISZ,K.LANG,R.MICURA,P.DUMAS,E.ENNIFAR JRNL TITL BINDING OF AMINOGLYCOSIDE ANTIBIOTICS TO THE JRNL TITL 2 DUPLEX FORM OF THE HIV-1 GENOMIC RNA DIMERIZATION JRNL TITL 3 INITIATION SITE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 47 4110 2008 JRNL REFN ISSN 0570-0833 JRNL PMID 18435520 JRNL DOI 10.1002/ANIE.200800726
REMARK 1
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) : 26.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 834219.640 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 9315 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) : 0.224 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT : 762 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) (%) : 83.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1267 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 108 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 978 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : -0.51000 REMARK 3 B33 (A**2) : 0.91000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 9.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.39 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 : 0.44 REMARK 3 BSOL : 66.59 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 : DNA-RNA_MULTI_END.PARAM REMARK 3 PARAMETER FILE 2 : PAROMOMYCINE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA_MULTI_END.TOP REMARK 3 TOPOLOGY FILE 2 : PAROMOMYCINE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3C44 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-08. REMARK 100 THE RCSB ID CODE IS RCSB046316.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-04 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 : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9195 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9333 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 (%) : 92.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.7000 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 (%) : 77.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.17000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.200 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: 3C3Z REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MGCL2, KCL, NA CACODYLATE, PH REMARK 280 6.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 310K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 15.40900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.85150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.40900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.85150 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: 5750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 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 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 A 96 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 63 LIES ON A SPECIAL POSITION.
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 54 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 91 DISTANCE = 5.39 ANGSTROMS
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 A A 8 O4' REMARK 620 2 HOH A 91 O 137.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 25 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 3 O4 REMARK 620 2 G B 4 O6 70.3 REMARK 620 3 HOH B 34 O 76.3 83.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 26 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PAR B 24 N32 REMARK 620 2 HOH B 62 O 101.9 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 PAR B 24 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PAR A 24 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 25 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 25 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 26 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 27 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 28
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QEK RELATED DB: PDB REMARK 900 FREE SUBTYPE F HIV-1 DIS EXTENDED DUPLEX RNA REMARK 900 RELATED ID: 3C3Z RELATED DB: PDB REMARK 900 RELATED ID: 3C5D RELATED DB: PDB
DBREF 3C44 A 1 23 PDB 3C44 3C44 1 23 DBREF 3C44 B 1 23 PDB 3C44 3C44 1 23
SEQRES 1 A 23 C U U 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 U G C U G A A G U G C SEQRES 2 B 23 A C A C A G C A A G
HET PAR A 24 42 HET PAR B 24 42 HET K A 25 1 HET CL A 26 1 HET K B 25 1 HET K B 26 1 HET CL B 27 1 HET K B 28 1
HETNAM PAR PAROMOMYCIN HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION
HETSYN PAR PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, HETSYN 2 PAR MONOMYCIN A, NEOMYCIN E
FORMUL 3 PAR 2(C23 H45 N5 O14) FORMUL 5 K 4(K 1+) FORMUL 6 CL 2(CL 1-) FORMUL 11 HOH *139(H2 O)
LINK O4' A A 8 K K A 25 1555 1555 2.95 LINK O4 U B 3 K K B 25 1555 1555 2.68 LINK O6 G B 4 K K B 25 1555 1555 2.66 LINK N32 PAR B 24 K K B 26 1555 1555 2.88 LINK K K A 25 O HOH A 91 1555 1555 2.85 LINK K K B 25 O HOH B 34 1555 1555 2.74 LINK K K B 26 O HOH B 62 1555 1555 2.87 LINK K K B 28 O HOH B 66 1555 1555 2.91
SITE 1 AC1 12 HOH A 31 HOH A 68 HOH B 30 HOH B 31 SITE 2 AC1 12 HOH B 35 HOH B 36 HOH B 43 HOH B 47 SITE 3 AC1 12 HOH B 58 HOH B 59 HOH B 62 HOH B 96 SITE 1 AC2 6 HOH A 29 HOH A 36 HOH A 72 HOH B 33 SITE 2 AC2 6 HOH B 43 HOH B 92 SITE 1 AC3 1 HOH A 91 SITE 1 AC4 1 HOH B 34 SITE 1 AC5 1 HOH B 62 SITE 1 AC6 1 HOH B 48 SITE 1 AC7 1 HOH B 66
CRYST1 30.818 95.703 47.856 90.00 90.00 90.00 P 21 21 2 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 0.032449 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010449 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020896 0.00000