HEADER RNA/ANTIBIOTIC 13-MAY-07 2PWT TITLE CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE COMPLEXED TITLE 2 WITH AMINOGLYCOSIDE CONTAINING THE L-HABA GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 22-MER OF THE RIBOSOMAL DECODING SITE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS AMINOGLYCOSIDE; HABA GROUP; RIBOSOMAL DECODING SITE; X-RAY ANALYSIS; KEYWDS 2 RNA, RNA-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,K.PACHAMUTHU,B.FRANCOIS,J.SZYCHOWSKI,S.HANESSIAN,E.WESTHOF REVDAT 6 13-MAR-24 2PWT 1 SOURCE REVDAT 5 30-AUG-23 2PWT 1 REMARK REVDAT 4 09-MAR-22 2PWT 1 REMARK HETSYN REVDAT 3 24-FEB-09 2PWT 1 VERSN REVDAT 2 20-NOV-07 2PWT 1 JRNL REVDAT 1 18-SEP-07 2PWT 0 JRNL AUTH J.KONDO,K.PACHAMUTHU,B.FRANCOIS,J.SZYCHOWSKI,S.HANESSIAN, JRNL AUTH 2 E.WESTHOF JRNL TITL CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE JRNL TITL 2 COMPLEXED WITH A SYNTHETIC DOUBLY FUNCTIONALIZED PAROMOMYCIN JRNL TITL 3 DERIVATIVE: A NEW SPECIFIC BINDING MODE TO AN A-MINOR MOTIF JRNL TITL 4 ENHANCES IN VITRO ANTIBACTERIAL ACTIVITY JRNL REF CHEMMEDCHEM V. 2 1631 2007 JRNL REFN ISSN 1860-7179 JRNL PMID 17722211 JRNL DOI 10.1002/CMDC.200700113 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : PARKINSON ET AL ACTA CRYST. D52, 57 (1996) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 14603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 15.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2272 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 900 REMARK 3 HETEROGEN ATOMS : 180 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.20400 REMARK 3 B22 (A**2) : 2.91800 REMARK 3 B33 (A**2) : -0.71400 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.664 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.380 ; 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 38.11 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 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : LHA_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : LHA_XPLOR.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PWT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000042864. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14605 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 32.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 1J7T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CACODYLATE (PH 6.4), 150 MM REMARK 280 KCL, 1% GLYCEROL, 1% 2-METHYL-2,4-PENTANDIOL, PH 6.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.74500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.37500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.37500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.74500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.51000 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 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 2 P G A 2 OP3 -0.084 REMARK 500 G B 24 P G B 24 OP3 -0.082 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LHA B 50 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LHA A 51 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LHA B 55 DBREF 2PWT A 2 22 PDB 2PWT 2PWT 2 22 DBREF 2PWT B 24 44 PDB 2PWT 2PWT 24 44 SEQRES 1 A 21 G C G U C A C A C C G G U SEQRES 2 A 21 G A A G U C G C SEQRES 1 B 21 G C G U C A C A C C G G U SEQRES 2 B 21 G A A G U C G C HET LHA A 51 60 HET LHA B 50 60 HET LHA B 55 60 HETNAM LHA DOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162 HETSYN LHA (2S)-4-AMINO-N-[(1R,2S,3R,4R,5S)-5-AMINO-4-[(2-AMINO-2- HETSYN 2 LHA DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-{[3-O-(2,6- HETSYN 3 LHA DIAMINO-2,6-DIDEO XY-BETA-L-IDOPYRANOSYL)-2-O-{2-[(2- HETSYN 4 LHA PHENYLETHYL)AMINO]ETHYL}-BETA-D-RIBOFURANOSYL]OXY}-2- HETSYN 5 LHA HYDROXYCYCLOHEXYL]-2-HYDROXYBUTA NAMIDE FORMUL 3 LHA 3(C37 H65 N7 O16) FORMUL 6 HOH *206(H2 O) SITE 1 AC1 25 G A 2 C A 3 U A 5 C A 6 SITE 2 AC1 25 A A 7 HOH A 165 G B 35 U B 36 SITE 3 AC1 25 G B 37 A B 38 A B 39 G B 40 SITE 4 AC1 25 U B 41 C B 42 G B 43 HOH B 103 SITE 5 AC1 25 HOH B 110 HOH B 118 HOH B 139 HOH B 164 SITE 6 AC1 25 HOH B 180 HOH B 183 HOH B 209 HOH B 249 SITE 7 AC1 25 HOH B 290 SITE 1 AC2 28 G A 13 U A 14 G A 15 A A 16 SITE 2 AC2 28 A A 17 G A 18 U A 19 C A 20 SITE 3 AC2 28 G A 21 C A 22 HOH A 101 HOH A 105 SITE 4 AC2 28 HOH A 111 HOH A 123 HOH A 153 HOH A 167 SITE 5 AC2 28 HOH A 168 HOH A 170 HOH A 191 HOH A 200 SITE 6 AC2 28 HOH A 223 HOH A 301 U B 27 C B 28 SITE 7 AC2 28 A B 29 LHA B 55 HOH B 194 HOH B 196 SITE 1 AC3 27 G A 12 A A 16 C A 20 G A 21 SITE 2 AC3 27 LHA A 51 HOH A 144 HOH A 185 HOH A 191 SITE 3 AC3 27 G B 34 G B 35 A B 38 A B 39 SITE 4 AC3 27 U B 41 C B 42 G B 43 C B 44 SITE 5 AC3 27 HOH B 125 HOH B 133 HOH B 148 HOH B 157 SITE 6 AC3 27 HOH B 169 HOH B 177 HOH B 192 HOH B 193 SITE 7 AC3 27 HOH B 194 HOH B 254 HOH B 278 CRYST1 35.490 43.020 98.750 90.00 90.00 90.00 P 21 21 21 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 0.028177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010127 0.00000