HEADER RNA 27-FEB-18 5ZEI TITLE CRYSTAL STRUCTURE OF THE BACTERIAL A1408ME1A-MUTANT RIBOSOMAL DECODING TITLE 2 SITE IN COMPLEX WITH GENETICIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA) COMPND 3 P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*GP*CP*GP*UP*CP*(1MA) COMPND 8 P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS RIBOSOME, RNA, AMINOGLYCOSIDE, ANTIBIOTIC-RESISTANCE EXPDTA X-RAY DIFFRACTION AUTHOR H.KANAZAWA,F.BABA,M.KOGANEI,J.KONDO REVDAT 2 22-NOV-23 5ZEI 1 REMARK REVDAT 1 21-MAR-18 5ZEI 0 SPRSDE 21-MAR-18 5ZEI 4WCQ JRNL AUTH H.KANAZAWA,F.BABA,M.KOGANEI,J.KONDO JRNL TITL A STRUCTURAL BASIS FOR THE ANTIBIOTIC RESISTANCE CONFERRED JRNL TITL 2 BY AN N1-METHYLATION OF A1408 IN 16S RRNA. JRNL REF NUCLEIC ACIDS RES. V. 45 12529 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 29036479 JRNL DOI 10.1093/NAR/GKX882 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 8418 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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 44.9002 - 3.8151 0.97 1334 175 0.1518 0.1895 REMARK 3 2 3.8151 - 3.0284 0.97 1250 159 0.1875 0.2350 REMARK 3 3 3.0284 - 2.6456 0.95 1240 138 0.2756 0.3480 REMARK 3 4 2.6456 - 2.4038 0.97 1235 134 0.2614 0.3351 REMARK 3 5 2.4038 - 2.2315 0.96 1211 157 0.2527 0.3220 REMARK 3 6 2.2315 - 2.0999 0.98 1247 138 0.2631 0.3301 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.21 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 : 0.021 1098 REMARK 3 ANGLE : 1.621 1706 REMARK 3 CHIRALITY : 0.672 243 REMARK 3 PLANARITY : 0.019 43 REMARK 3 DIHEDRAL : 12.953 500 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 5ZEI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-13 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 : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : D*TREK REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR, D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8419 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 44.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36500 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: PHENIX, PHASER REMARK 200 STARTING MODEL: 3TD1 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: SODIUM CACODYLATE, SPERMINE, MPD, REMARK 280 AMMONIUM CHLORIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 16.71500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.71500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.89000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 269 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 253 LIES ON A SPECIAL POSITION. REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 276 DISTANCE = 7.74 ANGSTROMS REMARK 525 HOH B 266 DISTANCE = 5.93 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GET A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GET B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ZEG RELATED DB: PDB DBREF 5ZEI A 2 23 PDB 5ZEI 5ZEI 2 23 DBREF 5ZEI B 26 46 PDB 5ZEI 5ZEI 26 46 SEQRES 1 A 22 U G C G U C 1MA C G U C G A SEQRES 2 A 22 C G A A G U C G C SEQRES 1 B 21 G C G U C 1MA C G U C G A C SEQRES 2 B 21 G A A G U C G C HET 1MA A 8 23 HET 1MA B 31 23 HET GET A 101 34 HET GET B 101 34 HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM GET GENETICIN HETSYN GET G418 FORMUL 1 1MA 2(C11 H16 N5 O7 P) FORMUL 3 GET 2(C20 H40 N4 O10) FORMUL 5 HOH *142(H2 O) LINK O3' C A 7 P 1MA A 8 1555 1555 1.61 LINK O3' 1MA A 8 P C A 9 1555 1555 1.60 LINK O3' C B 30 P 1MA B 31 1555 1555 1.61 LINK O3' 1MA B 31 P C B 32 1555 1555 1.61 SITE 1 AC1 17 G A 16 A A 17 A A 18 G A 19 SITE 2 AC1 17 U A 20 HOH A 212 HOH A 214 HOH A 238 SITE 3 AC1 17 HOH A 240 HOH A 242 HOH A 252 C B 27 SITE 4 AC1 17 G B 28 U B 29 C B 30 1MA B 31 SITE 5 AC1 17 C B 32 SITE 1 AC2 16 C A 4 G A 5 U A 6 C A 7 SITE 2 AC2 16 1MA A 8 C A 9 G B 39 A B 40 SITE 3 AC2 16 A B 41 G B 42 U B 43 HOH B 206 SITE 4 AC2 16 HOH B 211 HOH B 213 HOH B 215 HOH B 238 CRYST1 33.430 89.780 46.830 90.00 90.00 90.00 P 21 21 2 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 0.029913 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021354 0.00000