HEADER RIBOSOME 16-MAR-00 1EMI TITLE STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMAL TITLE 2 PROTEIN S8. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 16S RIBOSOMAL RNA; COMPND 3 CHAIN: B; COMPND 4 OTHER_DETAILS: COORDINATES FOR THERMUS THERMOPHILUS 16S COMPND 5 RRNA BUT SEQUENCE AND NUMBERING IS THAT OF E.COLI 16S RRNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RIBOSOMAL PROTEIN S8; COMPND 8 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 6 ORGANISM_TAXID: 274 KEYWDS RNA, RRNA, RIBOSOME, RIBOSOMAL PROTEIN, 16S RRNA, S8 EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A; P ATOMS ONLY, CHAIN B AUTHOR L.LANCASTER,G.M.CULVER,G.Z.YUSUPOVA,J.H.CATE,M.M.YUSPOV, AUTHOR 2 H.F.NOLLER REVDAT 4 24-FEB-09 1EMI 1 VERSN REVDAT 3 01-APR-03 1EMI 1 JRNL REVDAT 2 19-JUN-00 1EMI 3 SCALE1 SCALE2 SCALE3 REMARK REVDAT 1 12-JUN-00 1EMI 0 JRNL AUTH L.LANCASTER,G.M.CULVER,G.Z.YUSUPOVA,J.H.CATE, JRNL AUTH 2 M.M.YUSUPOV,H.F.NOLLER JRNL TITL THE LOCATION OF PROTEIN S8 AND SURROUNDING JRNL TITL 2 ELEMENTS OF 16S RRNA IN THE 70S RIBOSOME FROM JRNL TITL 3 COMBINED USE OF DIRECTED HYDROXYL RADICAL PROBING JRNL TITL 4 AND X-RAY CRYSTALLOGRAPHY. JRNL REF RNA V. 6 717 2000 JRNL REFN ISSN 1355-8382 JRNL PMID 10836793 JRNL DOI 10.1017/S1355838200000303 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 7.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 7.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 136 REMARK 3 NUCLEIC ACID ATOMS : 161 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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) : 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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: ALL DATA COLLECTION PARAMETERS ARE REMARK 3 AS REPORTED FOR 486D. THE RNA MODEL FOR THE S8 REGION OF 16S REMARK 3 RRNA WAS BUILT MANUALLY BY FITTING TO THE 7.8 A X-RAY MAP OF REMARK 3 THE THERMUS THERMOPHILUS 70S RIBOSOME (CATE ET AL., SCIENCE REMARK 3 285, 2095-2104, 1999; SEE PDB 486D) USING A SINGLE P REMARK 3 PSEUDOATOM FOR EACH NUCLEOTIDE. NOTE THAT THE NUCLEOTIDE REMARK 3 NUMBERING CORRESPONDS TO THE NUCLEOTIDE POSITIONS OF E.COLI REMARK 3 16S RRNA. PROTEIN S8 FROM THERMUS THERMOPHILUS (PDB 1AN7) WAS REMARK 3 FITTED TO THE 7.8 A MAP OF THE THERMUS THERMOPHILUS 70S REMARK 3 RIBOSOME BY SPLITTING THE PROTEIN INTO N- AND C-TERMINAL REMARK 3 DOMAINS BETWEEN RESIDUES 80 AND 81. THE TWO DOMAINS WERE FIT REMARK 3 SEPARATELY, RESULTING IN A SMALL RELATIVE MOVEMENT COMPARED REMARK 3 WITH THE ORIGINAL X-RAY STRUCTURE. ONLY C-ALPHA POSITIONS ARE REMARK 3 GIVEN IN THE PDB FILE. REMARK 4 REMARK 4 1EMI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-00. REMARK 100 THE RCSB ID CODE IS RCSB010724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 5 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1051 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 7.500 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 254.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 401.50000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 254.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 401.50000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 254.00000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 401.50000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 254.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 401.50000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 254.00000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 401.50000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 254.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 401.50000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 254.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 401.50000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 254.00000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 254.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 401.50000 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: B, A 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 486D RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL REMARK 900 COMPLEXES DBREF 1EMI A 3 138 UNP Q5SHQ2 RS8_THET8 3 138 DBREF 1EMI B 577 879 PDB 1EMI 1EMI 577 879 SEQADV 1EMI ASP A 25 UNP Q5SHQ2 GLU 25 CONFLICT SEQADV 1EMI ARG A 37 UNP Q5SHQ2 LYS 37 CONFLICT SEQADV 1EMI ASP A 52 UNP Q5SHQ2 GLU 52 CONFLICT SEQADV 1EMI VAL A 61 UNP Q5SHQ2 ILE 61 CONFLICT SEQADV 1EMI TYR A 62 UNP Q5SHQ2 HIS 62 CONFLICT SEQADV 1EMI HIS A 81 UNP Q5SHQ2 LYS 81 CONFLICT SEQADV 1EMI LYS A 88 UNP Q5SHQ2 ARG 88 CONFLICT SEQADV 1EMI SER A 115 UNP Q5SHQ2 PRO 115 CONFLICT SEQRES 1 B 161 G C A C G C A G G C G G U SEQRES 2 B 161 U U G U U A A G U C A G A SEQRES 3 B 161 U G U G A A A U C C C C G SEQRES 4 B 161 G G C U C A A C C U G G G SEQRES 5 B 161 A A C U G C A U C U G A U SEQRES 6 B 161 A C U G G C A A G C U U G SEQRES 7 B 161 A G U C U C G U A C G A A SEQRES 8 B 161 G A C U G A C G C U C A G SEQRES 9 B 161 G U G C G U C G A C U U G SEQRES 10 B 161 G A G G U U G U G C U U C SEQRES 11 B 161 G U G G C U U C C G G A G SEQRES 12 B 161 C U A A C G C G U U A A G SEQRES 13 B 161 U C G A C SEQRES 1 A 136 THR ASP PRO ILE ALA ASP MET LEU THR ARG ILE ARG ASN SEQRES 2 A 136 ALA THR ARG VAL TYR LYS GLU SER THR ASP VAL PRO ALA SEQRES 3 A 136 SER ARG PHE LYS GLU GLU ILE LEU ARG ILE LEU ALA ARG SEQRES 4 A 136 GLU GLY PHE ILE LYS GLY TYR GLU ARG VAL ASP VAL ASP SEQRES 5 A 136 GLY LYS PRO TYR LEU ARG VAL TYR LEU LYS TYR GLY PRO SEQRES 6 A 136 ARG ARG GLN GLY PRO ASP PRO ARG PRO GLU GLN VAL ILE SEQRES 7 A 136 HIS HIS ILE ARG ARG ILE SER LYS PRO GLY ARG ARG VAL SEQRES 8 A 136 TYR VAL GLY VAL LYS GLU ILE PRO ARG VAL ARG ARG GLY SEQRES 9 A 136 LEU GLY ILE ALA ILE LEU SER THR SER LYS GLY VAL LEU SEQRES 10 A 136 THR ASP ARG GLU ALA ARG LYS LEU GLY VAL GLY GLY GLU SEQRES 11 A 136 LEU ILE CYS GLU VAL TRP CRYST1 508.000 508.000 803.000 90.00 90.00 90.00 I 4 2 2 16 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 0.001969 0.000000 0.000000 0.00000 SCALE2 0.000000 0.001969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001245 0.00000