HEADER RNA 26-DEC-17 5Z1H TITLE CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE IN COMPLEX TITLE 2 WITH 6'-FLUORO SISOMICIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP* COMPND 4 C)-3'); COMPND 5 CHAIN: A, B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RRNA, AMINOGLYCOSIDE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR H.KANAZAWA,S.HANESSIAN,J.KONDO REVDAT 3 27-MAR-24 5Z1H 1 REMARK REVDAT 2 05-SEP-18 5Z1H 1 JRNL REVDAT 1 30-MAY-18 5Z1H 0 JRNL AUTH H.KANAZAWA,O.M.SAAVEDRA,J.P.MAIANTI,S.A.YOUNG,L.IZQUIERDO, JRNL AUTH 2 T.K.SMITH,S.HANESSIAN,J.KONDO JRNL TITL STRUCTURE-BASED DESIGN OF A EUKARYOTE-SELECTIVE JRNL TITL 2 ANTIPROTOZOAL FLUORINATED AMINOGLYCOSIDE. JRNL REF CHEMMEDCHEM V. 13 1541 2018 JRNL REFN ESSN 1860-7187 JRNL PMID 29766661 JRNL DOI 10.1002/CMDC.201800166 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 5047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.810 REMARK 3 FREE R VALUE TEST SET COUNT : 495 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.7603 - 3.8092 0.99 1175 113 0.1881 0.2173 REMARK 3 2 3.8092 - 3.0237 1.00 1136 125 0.1903 0.2544 REMARK 3 3 3.0237 - 2.6416 1.00 1108 132 0.2737 0.3230 REMARK 3 4 2.6416 - 2.4001 1.00 1133 125 0.2922 0.3421 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.16 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1027 REMARK 3 ANGLE : 1.008 1593 REMARK 3 CHIRALITY : 0.097 220 REMARK 3 PLANARITY : 0.020 42 REMARK 3 DIHEDRAL : 11.549 496 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Z1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006290. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.4SSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5052 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.540 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.61 REMARK 200 R MERGE FOR SHELL (I) : 0.27200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-METHYL-2,4-PENTANEDIOL, LICL, REMARK 280 SPERMINE TETRAHYDROCHLORIDE, SODIUM CACODYLATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 15.83250 REMARK 290 SMTRY3 2 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: 2280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 U A 1 REMARK 465 U A 2 REMARK 465 A A 17 REMARK 465 A A 18 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FSJ A 301 DBREF 5Z1H A 1 23 PDB 5Z1H 5Z1H 1 23 DBREF 5Z1H B 24 46 PDB 5Z1H 5Z1H 24 46 SEQRES 1 A 23 U U G C G U C A C G C C G SEQRES 2 A 23 G C G A A G U C G C SEQRES 1 B 23 U U G C G U C A C G C C G SEQRES 2 B 23 G C G A A G U C G C HET FSJ A 301 31 HETNAM FSJ (1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6- HETNAM 2 FSJ (FLUOROMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2- HETNAM 3 FSJ HYDROXYCYCLOHEXYL 3-DEOXY-4-C-METHYL-3-(METHYLAMINO)- HETNAM 4 FSJ BETA-L-ARABINOPYRANOSIDE HETSYN FSJ 6'-FLUORO SISOMICIN FORMUL 3 FSJ C19 H35 F N4 O7 FORMUL 4 HOH *87(H2 O) SITE 1 AC1 13 C A 4 G A 5 U A 6 C A 7 SITE 2 AC1 13 A A 8 C A 9 HOH A 401 HOH A 407 SITE 3 AC1 13 G B 39 A B 40 A B 41 G B 42 SITE 4 AC1 13 U B 43 CRYST1 42.905 31.665 46.696 90.00 94.82 90.00 P 1 21 1 4 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 0.023307 0.000000 0.001965 0.00000 SCALE2 0.000000 0.031581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021491 0.00000