HEADER RNA/ANTIBIOTIC 24-OCT-05 2BEE TITLE COMPLEX BETWEEN PAROMOMYCIN DERIVATIVE JS4 AND THE 16S-RRNA A SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP COMPND 3 *UP*CP*GP*C)-3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: EUBACTERIAL 16S RRNA A SITE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOMYCES RIMOSUS SUBSP. PAROMOMYCINUS; SOURCE 4 ORGANISM_TAXID: 92743 KEYWDS RNA-AMINOGLYCOSIDE INTERACTIONS, A SITE, UOU PAIRS, AA BULGES, RNA- KEYWDS 2 ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.FRANCOIS,E.WESTHOF REVDAT 5 13-MAR-24 2BEE 1 SOURCE REVDAT 4 23-AUG-23 2BEE 1 REMARK REVDAT 3 09-MAR-22 2BEE 1 COMPND REMARK HETNAM HETSYN REVDAT 2 24-FEB-09 2BEE 1 VERSN REVDAT 1 20-DEC-05 2BEE 0 JRNL AUTH B.FRANCOIS,J.SZYCHOWSKI,S.S.ADHIKARI,K.PACHAMUTHU, JRNL AUTH 2 E.E.SWAYZE,R.H.GRIFFEY,M.T.MIGAWA,E.WESTHOF,S.HANESSIAN JRNL TITL ANTIBACTERIAL AMINOGLYCOSIDES WITH A MODIFIED MODE OF JRNL TITL 2 BINDING TO THE RIBOSOMAL-RNA DECODING SITE JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 43 6735 2004 JRNL REFN ESSN 0570-0833 JRNL PMID 15593140 JRNL DOI 10.1002/ANIE.200462092 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 : G. PARKINSON, J. VOJTECHOVSKY, L. REMARK 3 CLOWNEY,A.T. BRUNGER, H.M. BERMAN, NEW REMARK 3 PARAMETERSFOR THE REFINEMENT OF NUCLEIC ACID REMARK 3 CONTAINING STRUCTURES, ACTA CRYST. D, 52,57- REMARK 3 64 (1996) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4433 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) : 0.220 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 471 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 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 : 898 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM SIGMAA (A) : 0.55 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) : 0.53 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 10.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.249 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) : 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BEE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1000034996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 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 : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL 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 1J7T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, KCL, MGSO4, GLYCEROL, NA REMARK 280 CACODYLATE, PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 49.51350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.75675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.27025 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 C A 0 REMARK 465 C B 21 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JS4 A 50 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JS4 B 51 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J7T RELATED DB: PDB REMARK 900 COMPLEX BETWEEN NATURAL PAROMOMYCIN AMD THE 16S-RRNA A SITE REMARK 900 RELATED ID: 2ESI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN KANAMYCIN A AND THE 16S- REMARK 900 RRNA A SITE REMARK 900 RELATED ID: 2BE0 RELATED DB: PDB REMARK 900 COMPLEX BETWEEN PAROMOMYCIN DERIVATIVE JS5-39 AND THE 16S-RRNA A- REMARK 900 SITE REMARK 900 RELATED ID: 2ESJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN LIVIDOMYCIN A AND THE 16S- REMARK 900 RRNA A SITE DBREF 2BEE A 0 21 PDB 2BEE 2BEE 0 21 DBREF 2BEE B 21 42 PDB 2BEE 2BEE 21 42 SEQRES 1 A 22 C G C G U C A C A C C G G SEQRES 2 A 22 U G A A G U C G C SEQRES 1 B 22 C G C G U C A C A C C G G SEQRES 2 B 22 U G A A G U C G C HET JS4 A 50 49 HET JS4 B 51 49 HETNAM JS4 (2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R, HETNAM 2 JS4 5S)-4-(2-(3-AMINOPROPYLAMINO)ETHOXY)-5-((1R,2R,3S,5R, HETNAM 3 JS4 6S)-3,5-DIAM INO-2-((2S,3R,4R,5S,6R)-3-AMINO-4,5- HETNAM 4 JS4 DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2- HETNAM 5 JS4 YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-( HYDROXYMETHYL)- HETNAM 6 JS4 TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL HETSYN JS4 2"-O-[N-(3-(AMINOPROPYL)2-AMINOETHYL]PAROMOMYCIN; O-2- HETSYN 2 JS4 AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL-(1,4)-O-[O-2,6- HETSYN 3 JS4 DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSYL-(1,3)-BETA-D- HETSYN 4 JS4 2-O-(2-(1,3 -DIAMINOPROPYL)-ETHYL)-RIBOFURANOSYL-(1, HETSYN 5 JS4 5)-2-DEOXY-D-STREPTAMINE FORMUL 3 JS4 2(C28 H57 N7 O14) FORMUL 5 HOH *63(H2 O) SITE 1 AC1 16 U A 13 G A 14 A A 15 A A 16 SITE 2 AC1 16 G A 17 U A 18 HOH A 100 HOH A 109 SITE 3 AC1 16 HOH A 127 HOH A 129 HOH A 133 HOH A 148 SITE 4 AC1 16 U B 25 C B 26 A B 27 A B 29 SITE 1 AC2 13 U A 4 C A 5 A A 6 A A 8 SITE 2 AC2 13 U B 34 G B 35 A B 36 A B 37 SITE 3 AC2 13 G B 38 U B 39 HOH B 107 HOH B 120 SITE 4 AC2 13 HOH B 152 CRYST1 39.171 39.171 99.027 90.00 90.00 90.00 P 41 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 0.025529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010098 0.00000