HEADER RNA/ANTIBIOTIC 10-APR-13 4K31 TITLE CRYSTAL STRUCTURE OF APRAMYCIN BOUND TO THE LEISHMANIAL RRNA A-SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP* COMPND 4 C)-3'); COMPND 5 CHAIN: B, C; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: LEISHMANIA; SOURCE 4 ORGANISM_TAXID: 38568 KEYWDS RRNA DUPLEX, RIBOSOMAL A-SITE, AMINOGLYCOSIDE, RIBOSOME, RNA, RNA- KEYWDS 2 ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.SHALEV,J.KONDO,N.ADIR,T.BAASOV REVDAT 3 20-SEP-23 4K31 1 REMARK HETSYN REVDAT 2 04-SEP-13 4K31 1 JRNL REVDAT 1 31-JUL-13 4K31 0 JRNL AUTH M.SHALEV,J.KONDO,D.KOPELYANSKIY,C.L.JAFFE,N.ADIR,T.BAASOV JRNL TITL IDENTIFICATION OF THE MOLECULAR ATTRIBUTES REQUIRED FOR JRNL TITL 2 AMINOGLYCOSIDE ACTIVITY AGAINST LEISHMANIA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 13333 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23898171 JRNL DOI 10.1073/PNAS.1307365110 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 23271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 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 19.5116 - 2.8276 0.60 1740 94 0.2566 0.3155 REMARK 3 2 2.8276 - 2.2454 0.99 2912 159 0.2219 0.2846 REMARK 3 3 2.2454 - 1.9619 1.00 2904 167 0.2052 0.2239 REMARK 3 4 1.9619 - 1.7826 1.00 2941 137 0.2114 0.2291 REMARK 3 5 1.7826 - 1.6549 1.00 2908 157 0.2077 0.2234 REMARK 3 6 1.6549 - 1.5574 1.00 2921 144 0.2165 0.2402 REMARK 3 7 1.5574 - 1.4795 1.00 2929 167 0.2222 0.2323 REMARK 3 8 1.4795 - 1.4151 0.98 2826 165 0.2456 0.2827 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.60 REMARK 3 B_SOL : 80.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.400 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) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 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 : 0.006 1208 REMARK 3 ANGLE : 0.976 1872 REMARK 3 CHIRALITY : 0.051 288 REMARK 3 PLANARITY : 0.009 44 REMARK 3 DIHEDRAL : 15.785 638 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 4K31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-12 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 : 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) : 0.9394 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 35.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 21.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2G5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA CACODYLATE, 1 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 1% 2-METHYL-2,4-PENTADIOL (VS. 40% RESERVOIR) REMARK 280 , 100-250 MM NACL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.80000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.60000 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: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 B 1 REMARK 465 U C 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AM2 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AM2 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AM2 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AM2 C 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K32 RELATED DB: PDB DBREF 4K31 B 1 23 PDB 4K31 4K31 1 23 DBREF 4K31 C 1 23 PDB 4K31 4K31 1 23 SEQRES 1 B 23 U U G C G U C G U U C C G SEQRES 2 B 23 G A A A A G U C G C SEQRES 1 C 23 U U G C G U C G U U C C G SEQRES 2 C 23 G A A A A G U C G C HET AM2 B 101 37 HET AM2 B 102 37 HET AM2 C 101 37 HET AM2 C 102 37 HETNAM AM2 APRAMYCIN HETSYN AM2 NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4- HETSYN 2 AM2 DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8, HETSYN 3 AM2 8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO) HETSYN 4 AM2 PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE FORMUL 3 AM2 4(C21 H41 N5 O11) FORMUL 7 HOH *209(H2 O) SITE 1 AC1 13 C B 4 G B 5 U B 6 G B 8 SITE 2 AC1 13 HOH B 207 HOH B 211 HOH B 239 HOH B 258 SITE 3 AC1 13 HOH B 295 A C 17 G C 19 U C 20 SITE 4 AC1 13 HOH C 219 SITE 1 AC2 24 U B 9 U B 10 C B 11 HOH B 205 SITE 2 AC2 24 HOH B 225 HOH B 232 HOH B 233 HOH B 235 SITE 3 AC2 24 HOH B 240 HOH B 253 HOH B 260 HOH B 274 SITE 4 AC2 24 HOH B 287 HOH B 297 HOH B 301 HOH B 308 SITE 5 AC2 24 G C 8 U C 9 C C 23 HOH C 201 SITE 6 AC2 24 HOH C 210 HOH C 215 HOH C 274 HOH C 280 SITE 1 AC3 23 G B 8 U B 9 C B 23 HOH B 210 SITE 2 AC3 23 HOH B 294 HOH B 308 U C 9 U C 10 SITE 3 AC3 23 C C 11 HOH C 202 HOH C 204 HOH C 205 SITE 4 AC3 23 HOH C 225 HOH C 236 HOH C 238 HOH C 240 SITE 5 AC3 23 HOH C 257 HOH C 262 HOH C 269 HOH C 270 SITE 6 AC3 23 HOH C 275 HOH C 283 HOH C 295 SITE 1 AC4 17 G B 14 A B 17 G B 19 U B 20 SITE 2 AC4 17 HOH B 218 HOH B 227 C C 4 G C 5 SITE 3 AC4 17 U C 6 G C 8 HOH C 216 HOH C 239 SITE 4 AC4 17 HOH C 247 HOH C 278 HOH C 282 HOH C 284 SITE 5 AC4 17 HOH C 296 CRYST1 32.790 32.790 107.400 90.00 90.00 120.00 P 31 6 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 0.030497 0.017608 0.000000 0.00000 SCALE2 0.000000 0.035215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009311 0.00000