HEADER RNA 26-OCT-05 2ESJ TITLE COMPLEX BETWEEN LIVIDOMYCIN A 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: BACTERIAL A-SITE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA-AMINOGLYCOSIDE INTERACTIONS, A SITE, UOU PAIRS, AA BULGES, RNA EXPDTA X-RAY DIFFRACTION AUTHOR E.WESTHOF REVDAT 3 14-FEB-24 2ESJ 1 COMPND REMARK HETNAM HETSYN REVDAT 2 24-FEB-09 2ESJ 1 VERSN REVDAT 1 20-DEC-05 2ESJ 0 JRNL AUTH B.FRANCOIS,R.J.M.RUSSEL,J.B.MURRAY,F.ABOUL-ELA,B.MASQUIDA, JRNL AUTH 2 Q.VICENS,E.WESTHOF JRNL TITL CRYSTAL STRUCTURES OF COMPLEXES BETWEEN AMINOGLYCOSIDES AND JRNL TITL 2 DECODING A SITE OLIGONUCLEOTIDES: ROLE OF THE NUMBER OF JRNL TITL 3 RINGS AND POSITIVE CHARGES IN THE SPECIFIC BINDING LEADING JRNL TITL 4 TO MISCODING JRNL REF NUCLEIC ACIDS RES. V. 33 5677 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16214802 JRNL DOI 10.1093/NAR/GKI862 REMARK 2 REMARK 2 RESOLUTION. 2.20 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. CLOWNEY, REMARK 3 A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR REMARK 3 THE REFINEMENT OF NUCLEIC ACID CONTAINING REMARK 3 STRUCTURES, ACTA CRYST. D, 52,57-64 (1996) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.4 REMARK 3 NUMBER OF REFLECTIONS : 6628 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) : 0.228 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 728 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 : 898 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 90 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) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 3.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 12.81 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.000 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 2ESJ 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_1000035039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.936 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7759 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, NACL, 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 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 16.83000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.79000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.28050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.79000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.83000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.28050 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 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 1 REMARK 465 C B 24 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 C B 29 C5' - C4' - C3' ANGL. DEV. = -8.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 A B 40 0.06 SIDE CHAIN 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 LIV A 50 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LIV B 51 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J7T RELATED DB: PDB REMARK 900 COMPLEX BETWEEN NATURAL PAROMOMYCIN AND 16S RRNA A SITE REMARK 900 RELATED ID: 2BEE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PAROMOMYCIN DERIVATIVE JS4 REMARK 900 AND THE 16S-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: 2ESI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN KANAMYCIN A AND THE 16S- REMARK 900 RRNA A SITE DBREF 2ESJ A 1 22 PDB 2ESJ 2ESJ 1 22 DBREF 2ESJ B 24 45 PDB 2ESJ 2ESJ 24 45 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 LIV A 50 52 HET LIV B 51 52 HETNAM LIV (2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2- HETNAM 2 LIV (AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3, HETNAM 3 LIV 5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6- HETNAM 4 LIV (HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6- HETNAM 5 LIV HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)- HETNAM 6 LIV TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H- HETNAM 7 LIV PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN- HETNAM 8 LIV 3,4,5-TRIOL HETSYN LIV LIVIDOMYCIN A; O-2-AMINO-2,3-DIDEOXY-ALPHA-D- HETSYN 2 LIV GLUCOPYRANOSYL-(1,4)-O-[BETA-D-MANNOPYRANOSYL-(1,4)-O- HETSYN 3 LIV 2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPY RANOSYL-(1,3)- HETSYN 4 LIV BETA-D-RIBOFURANOSYL-(1,5)-2-DEOXY-D-STREPTAMINE FORMUL 3 LIV 2(C29 H55 N5 O18) FORMUL 5 HOH *90(H2 O) SITE 1 AC1 12 U A 14 G A 15 A A 17 G A 18 SITE 2 AC1 12 U A 19 HOH A 101 HOH A 117 C B 26 SITE 3 AC1 12 G B 27 C B 29 A B 30 HOH B 100 SITE 1 AC2 22 C A 3 G A 4 U A 5 C A 6 SITE 2 AC2 22 A A 7 C A 20 U B 37 G B 38 SITE 3 AC2 22 A B 39 A B 40 G B 41 U B 42 SITE 4 AC2 22 HOH B 105 HOH B 113 HOH B 124 HOH B 128 SITE 5 AC2 22 HOH B 129 HOH B 130 HOH B 137 HOH B 143 SITE 6 AC2 22 HOH B 170 HOH B 189 CRYST1 33.660 44.561 95.580 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 0.029709 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010462 0.00000