HEADER RNA 23-FEB-06 2G5K TITLE CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING TITLE 2 SITE COMPLEXED WITH APRAMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP COMPND 3 *GP*UP*CP*GP*C)-3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS AMINOGLYCOSIDE, ANTIBIOTICS, APRAMYCIN, RIBOSOME, DECODING SITE, HOMO KEYWDS 2 SAPIENS, CYTOPLASM, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,B.FRANCOIS,A.URZHUMTSEV,E.WESTHOF REVDAT 3 13-MAR-24 2G5K 1 REMARK HETSYN LINK REVDAT 2 24-FEB-09 2G5K 1 VERSN REVDAT 1 20-JUN-06 2G5K 0 JRNL AUTH J.KONDO,B.FRANCOIS,A.URZHUMTSEV,E.WESTHOF JRNL TITL CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL JRNL TITL 2 DECODING SITE COMPLEXED WITH APRAMYCIN JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 45 3310 2006 JRNL REFN ESSN 0570-0833 JRNL PMID 16596680 JRNL DOI 10.1002/ANIE.200600354 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3437 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) : 0.258 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 347 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 389 REMARK 3 BIN R VALUE (WORKING SET) : 0.5530 REMARK 3 BIN FREE R VALUE : 0.5780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 34 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 : 938 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.93200 REMARK 3 B22 (A**2) : 7.93200 REMARK 3 B33 (A**2) : -15.86500 REMARK 3 B12 (A**2) : -1.14800 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.500 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 : 75.81 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 2 : AM2_XPLOR.PARAM REMARK 3 PARAMETER FILE 3 : NCO_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : MO6_XPLOR.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 2 : AM2_XPLOR.TOP REMARK 3 TOPOLOGY FILE 3 : NCO_XPLOR.TOP REMARK 3 TOPOLOGY FILE 4 : MO6_XPLOR.TOP REMARK 3 TOPOLOGY FILE 5 : WATER.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2G5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.9793 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3533 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 27.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.590 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.76 REMARK 200 R MERGE FOR SHELL (I) : 0.39700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 50.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM CACODYLATE, 10MM HEXAMMINE REMARK 280 COBALT CHLORIDE, 150MM POTASSIUM CHLORIDE, 1%(V/V) 2-METHYL-2,4- REMARK 280 PENTANEDIOL, 5%(V/V) GLYCEROL, PH 6.4, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 300K 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 38.80700 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 77.61400 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 U A 1 REMARK 465 U B 24 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 416 O REMARK 620 2 HOH A 417 O 179.8 REMARK 620 3 HOH A 419 O 90.0 89.9 REMARK 620 4 HOH A 420 O 90.0 89.9 90.2 REMARK 620 5 HOH A 421 O 89.8 90.3 89.9 179.8 REMARK 620 6 HOH B 418 O 90.1 90.0 179.8 89.9 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 424 O REMARK 620 2 HOH B 422 O 90.0 REMARK 620 3 HOH B 423 O 90.0 179.9 REMARK 620 4 HOH B 425 O 179.8 90.1 89.9 REMARK 620 5 HOH B 426 O 89.8 90.1 89.8 90.3 REMARK 620 6 HOH B 427 O 90.1 89.8 90.3 89.8 179.9 REMARK 620 N 1 2 3 4 5 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 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FQN RELATED DB: PDB DBREF 2G5K A 1 23 PDB 2G5K 2G5K 1 23 DBREF 2G5K B 24 46 PDB 2G5K 2G5K 24 46 SEQRES 1 A 23 U U G C G U C G C U C C G SEQRES 2 A 23 G A A A A G U C G C SEQRES 1 B 23 U U G C G U C G C U C C G SEQRES 2 B 23 G A A A A G U C G C HET AM2 A 102 37 HET MG A 301 1 HET NCO A 202 7 HET AM2 B 101 37 HET MG B 302 1 HET NCO B 201 7 HETNAM AM2 APRAMYCIN HETNAM MG MAGNESIUM ION HETNAM NCO COBALT HEXAMMINE(III) 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 2(C21 H41 N5 O11) FORMUL 4 MG 2(MG 2+) FORMUL 5 NCO 2(CO H18 N6 3+) FORMUL 9 HOH *27(H2 O) LINK MG MG A 301 O HOH A 416 1555 1555 2.07 LINK MG MG A 301 O HOH A 417 1555 1555 2.02 LINK MG MG A 301 O HOH A 419 1555 1555 2.07 LINK MG MG A 301 O HOH A 420 1555 1555 2.13 LINK MG MG A 301 O HOH A 421 1555 1555 2.12 LINK MG MG A 301 O HOH B 418 1555 1555 2.10 LINK O HOH A 424 MG MG B 302 1555 1555 2.10 LINK MG MG B 302 O HOH B 422 1555 1555 2.08 LINK MG MG B 302 O HOH B 423 1555 1555 2.02 LINK MG MG B 302 O HOH B 425 1555 1555 2.07 LINK MG MG B 302 O HOH B 426 1555 1555 2.13 LINK MG MG B 302 O HOH B 427 1555 1555 2.12 SITE 1 AC1 11 A A 15 A A 17 A A 18 G A 19 SITE 2 AC1 11 HOH A 415 C B 27 G B 28 U B 29 SITE 3 AC1 11 C B 30 G B 31 HOH B 407 SITE 1 AC2 11 C A 4 G A 5 U A 6 C A 7 SITE 2 AC2 11 G A 8 HOH A 405 A B 38 A B 40 SITE 3 AC2 11 A B 41 G B 42 HOH B 414 SITE 1 AC3 6 HOH A 416 HOH A 417 HOH A 419 HOH A 420 SITE 2 AC3 6 HOH A 421 HOH B 418 SITE 1 AC4 6 HOH A 424 HOH B 422 HOH B 423 HOH B 425 SITE 2 AC4 6 HOH B 426 HOH B 427 SITE 1 AC5 2 G B 36 G B 37 SITE 1 AC6 2 G A 13 G A 14 CRYST1 33.123 33.123 116.421 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 0.030191 0.017430 0.000000 0.00000 SCALE2 0.000000 0.034861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008590 0.00000