HEADER STRUCTURAL PROTEIN/RNA 24-NOV-04 1Y39 TITLE CO-EVOLUTION OF PROTEIN AND RNA STRUCTURES WITHIN A HIGHLY CONSERVED TITLE 2 RIBOSOMAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN; COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 8 CHAIN: A, B; COMPND 9 FRAGMENT: C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11; COMPND 10 SYNONYM: RIBOSOMAL PROTEIN L11; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: NTS 1051-1108 FROM E. COLI 23S RRNA; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 6 ORGANISM_TAXID: 1422; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PUC18; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: L11-C76(S69N) KEYWDS X-RAY CRYSTAL STRUCTURE, CHOROPLAST-LIKE L11 COMPLEX, RRNA, 23S RNA, KEYWDS 2 STRUCTURAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.S.DUNSTAN,D.GUHATHAKURTA,D.E.DRAPER,G.L.CONN REVDAT 5 25-OCT-23 1Y39 1 REMARK REVDAT 4 10-NOV-21 1Y39 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1Y39 1 VERSN REVDAT 2 24-FEB-09 1Y39 1 VERSN REVDAT 1 22-MAR-05 1Y39 0 JRNL AUTH M.S.DUNSTAN,D.GUHATHAKURTA,D.E.DRAPER,G.L.CONN JRNL TITL COEVOLUTION OF PROTEIN AND RNA STRUCTURES WITHIN A HIGHLY JRNL TITL 2 CONSERVED RIBOSOMAL DOMAIN JRNL REF CHEM.BIOL. V. 12 201 2005 JRNL REFN ISSN 1074-5521 JRNL PMID 15734647 JRNL DOI 10.1016/J.CHEMBIOL.2004.11.019 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1487462.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 17764 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1033 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2762 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1083 REMARK 3 NUCLEIC ACID ATOMS : 2500 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.75000 REMARK 3 B22 (A**2) : -1.75000 REMARK 3 B33 (A**2) : 3.51000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.54 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.56 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.460 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.870 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.600 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.070 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.760 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 43.77 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_GTP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : GOL.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_GTP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : GOL.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : RH COATED SI MIRROR REMARK 200 OPTICS : RH COATED SI MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17764 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : 0.44500 REMARK 200 FOR SHELL : 5.100 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: PDB ENTRY 1HC8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG600, MAGNESIUM ACETATE, GLYCEROL, REMARK 280 SODIUM CACODYLATE, POTASIUM CHLRORIDE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 310K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 31.49200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 75.12000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 75.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.23800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 75.12000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 75.12000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.74600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 75.12000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.12000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.23800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 75.12000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.12000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.74600 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 31.49200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: C, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 PHE A 1 REMARK 465 ASP A 76 REMARK 465 PHE B 201 REMARK 465 THR B 202 REMARK 465 PHE B 203 REMARK 465 ILE B 204 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 2 OG1 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 38 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C C 102 OP1 - P - OP2 ANGL. DEV. = -9.8 DEGREES REMARK 500 C C 102 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 C C 103 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 C D 302 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 C D 303 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 PRO B 227 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 35 -166.69 -122.01 REMARK 500 ALA B 233 169.76 173.90 REMARK 500 ARG B 237 -3.37 -49.28 REMARK 500 GLU B 257 -60.56 -90.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 A C 119 0.06 SIDE CHAIN REMARK 500 G C 137 0.07 SIDE CHAIN REMARK 500 U C 144 0.07 SIDE CHAIN REMARK 500 U C 147 0.07 SIDE CHAIN REMARK 500 U D 310 0.07 SIDE CHAIN REMARK 500 A D 319 0.07 SIDE CHAIN REMARK 500 A D 334 0.06 SIDE CHAIN REMARK 500 U D 347 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 C 407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U C 116 OP1 REMARK 620 2 A D 336 OP1 84.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 119 O3' REMARK 620 2 A C 120 OP2 50.9 REMARK 620 3 C C 122 OP1 113.6 62.7 REMARK 620 4 C C 122 O5' 146.2 101.4 43.9 REMARK 620 5 C C 122 OP2 104.9 73.0 49.8 42.3 REMARK 620 6 A C 123 OP1 147.9 153.1 94.9 65.6 104.8 REMARK 620 7 MG C 415 MG 82.5 33.2 33.1 76.7 67.2 120.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 415 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 120 OP2 REMARK 620 2 C C 122 OP1 96.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 123 OP2 REMARK 620 2 G C 143 O6 131.2 REMARK 620 3 U C 144 O4 158.2 69.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 421 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 136 O2' REMARK 620 2 G C 137 O6 85.8 REMARK 620 3 HOH C 807 O 74.2 122.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 411 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A D 307 N7 REMARK 620 2 A D 336 O2' 84.5 REMARK 620 3 G D 337 OP2 84.2 78.6 REMARK 620 4 G D 337 N7 158.2 75.8 83.1 REMARK 620 5 HOH D 810 O 96.9 59.2 137.4 80.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A D 319 O3' REMARK 620 2 A D 320 OP2 49.4 REMARK 620 3 C D 322 O5' 142.7 96.4 REMARK 620 4 C D 322 OP2 105.6 75.3 42.4 REMARK 620 5 C D 322 OP1 99.9 51.0 45.8 45.5 REMARK 620 6 A D 323 OP1 150.5 146.8 66.2 103.5 104.1 REMARK 620 7 GOL D 704 O1 94.9 130.7 100.3 86.7 132.2 81.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A D 320 OP2 REMARK 620 2 C D 322 OP1 71.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3CO D 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K D 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HC8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX DBREF 1Y39 A 1 76 UNP P56210 RL11_BACST 58 133 DBREF 1Y39 B 201 276 UNP P56210 RL11_BACST 58 133 DBREF 1Y39 C 101 158 PDB 1Y39 1Y39 101 158 DBREF 1Y39 D 301 358 PDB 1Y39 1Y39 301 358 SEQADV 1Y39 ASN A 69 UNP P56210 SER 126 ENGINEERED MUTATION SEQADV 1Y39 ASN B 269 UNP P56210 SER 126 ENGINEERED MUTATION SEQRES 1 C 58 GTP C C A G G A U G U A U G SEQRES 2 C 58 C U U A G A A G C A G C A SEQRES 3 C 58 A U C A U U U A A A G A G SEQRES 4 C 58 U G C G U A A U A G C U C SEQRES 5 C 58 A C U G G U SEQRES 1 D 58 GTP C C A G G A U G U A U G SEQRES 2 D 58 C U U A G A A G C A G C A SEQRES 3 D 58 A U C A U U U A A A G A G SEQRES 4 D 58 U G C G U A A U A G C U C SEQRES 5 D 58 A C U G G U SEQRES 1 A 76 PHE THR PHE ILE THR LYS THR PRO PRO ALA ALA VAL LEU SEQRES 2 A 76 LEU LYS LYS ALA ALA GLY ILE GLU SER GLY SER GLY GLU SEQRES 3 A 76 PRO ASN ARG ASN LYS VAL ALA THR ILE LYS ARG ASP LYS SEQRES 4 A 76 VAL ARG GLU ILE ALA GLU LEU LYS MET PRO ASP LEU ASN SEQRES 5 A 76 ALA ALA SER ILE GLU ALA ALA MET ARG MET ILE GLU GLY SEQRES 6 A 76 THR ALA ARG ASN MET GLY ILE VAL VAL GLU ASP SEQRES 1 B 76 PHE THR PHE ILE THR LYS THR PRO PRO ALA ALA VAL LEU SEQRES 2 B 76 LEU LYS LYS ALA ALA GLY ILE GLU SER GLY SER GLY GLU SEQRES 3 B 76 PRO ASN ARG ASN LYS VAL ALA THR ILE LYS ARG ASP LYS SEQRES 4 B 76 VAL ARG GLU ILE ALA GLU LEU LYS MET PRO ASP LEU ASN SEQRES 5 B 76 ALA ALA SER ILE GLU ALA ALA MET ARG MET ILE GLU GLY SEQRES 6 B 76 THR ALA ARG ASN MET GLY ILE VAL VAL GLU ASP MODRES 1Y39 GTP C 101 G GUANOSINE-5'-TRIPHOSPHATE MODRES 1Y39 GTP D 301 G GUANOSINE-5'-TRIPHOSPHATE HET GTP C 101 32 HET GTP D 301 32 HET 3CO C 402 1 HET K C 404 1 HET MG C 405 1 HET MG C 407 1 HET MG C 408 1 HET MG C 409 1 HET MG C 415 1 HET MG C 416 1 HET MG C 417 1 HET MG C 419 1 HET MG C 420 1 HET MG C 421 1 HET GOL C 705 6 HET 3CO D 401 1 HET K D 403 1 HET MG D 406 1 HET MG D 410 1 HET MG D 411 1 HET MG D 412 1 HET MG D 413 1 HET MG D 414 1 HET MG D 418 1 HET MG D 422 1 HET GOL D 704 6 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM 3CO COBALT (III) ION HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 GTP 2(C10 H16 N5 O14 P3) FORMUL 5 3CO 2(CO 3+) FORMUL 6 K 2(K 1+) FORMUL 7 MG 18(MG 2+) FORMUL 17 GOL 2(C3 H8 O3) FORMUL 29 HOH *15(H2 O) HELIX 1 1 PRO A 9 GLY A 19 1 11 HELIX 2 2 LYS A 36 MET A 48 1 13 HELIX 3 3 SER A 55 ASN A 69 1 15 HELIX 4 4 PRO B 209 ALA B 218 1 10 HELIX 5 5 LYS B 239 MET B 248 1 10 HELIX 6 6 PRO B 249 LEU B 251 5 3 HELIX 7 7 SER B 255 ASN B 269 1 15 SHEET 1 A 2 ALA A 33 ILE A 35 0 SHEET 2 A 2 ILE A 72 VAL A 74 1 O VAL A 73 N ILE A 35 SHEET 1 B 2 ALA B 233 LYS B 236 0 SHEET 2 B 2 ILE B 272 GLU B 275 1 O VAL B 273 N ILE B 235 LINK O3' GTP C 101 P C C 102 1555 1555 1.58 LINK O3' GTP D 301 P C D 302 1555 1555 1.60 LINK OP2 G C 113 MG MG C 408 1555 1555 2.27 LINK OP1 U C 116 MG MG C 407 1555 1555 2.17 LINK O3' A C 119 K K C 404 1555 1555 3.03 LINK OP2 A C 120 K K C 404 1555 1555 2.81 LINK OP2 A C 120 MG MG C 415 1555 1555 2.01 LINK OP1 C C 122 K K C 404 1555 1555 2.95 LINK O5' C C 122 K K C 404 1555 1555 3.62 LINK OP2 C C 122 K K C 404 1555 1555 3.12 LINK OP1 C C 122 MG MG C 415 1555 1555 1.99 LINK OP1 A C 123 K K C 404 1555 1555 2.81 LINK OP2 A C 123 MG MG C 405 1555 1555 1.99 LINK O2' A C 136 MG MG C 421 1555 1555 2.77 LINK O6 G C 137 MG MG C 421 1555 1555 2.88 LINK O6 G C 143 MG MG C 405 1555 1555 2.97 LINK O4 U C 144 MG MG C 405 1555 1555 2.07 LINK K K C 404 MG MG C 415 1555 1555 3.64 LINK MG MG C 407 OP1 A D 336 1555 1555 2.41 LINK MG MG C 409 O HOH C 806 1555 1555 2.20 LINK MG MG C 421 O HOH C 807 1555 1555 2.43 LINK N7 A D 307 MG MG D 411 1555 1555 3.11 LINK OP2 A D 311 MG MG D 418 1555 1555 2.95 LINK OP2 G D 313 MG MG D 422 1555 1555 2.62 LINK O3' A D 319 K K D 403 1555 1555 3.17 LINK OP2 A D 320 K K D 403 1555 1555 2.83 LINK OP2 A D 320 MG MG D 406 1555 1555 2.19 LINK O5' C D 322 K K D 403 1555 1555 3.34 LINK OP2 C D 322 K K D 403 1555 1555 3.47 LINK OP1 C D 322 K K D 403 1555 1555 3.11 LINK OP1 C D 322 MG MG D 406 1555 1555 2.21 LINK OP1 A D 323 K K D 403 1555 1555 2.78 LINK O2' A D 336 MG MG D 411 1555 1555 3.01 LINK OP2 G D 337 MG MG D 411 1555 1555 2.83 LINK N7 G D 337 MG MG D 411 1555 1555 3.15 LINK K K D 403 O1 GOL D 704 1555 1555 3.15 LINK MG MG D 410 O HOH D 811 1555 1555 2.41 LINK MG MG D 411 O HOH D 810 1555 1555 2.68 LINK MG MG D 412 O HOH D 809 1555 1555 2.54 SITE 1 AC1 1 G D 337 SITE 1 AC2 5 A D 319 A D 320 C D 322 A D 323 SITE 2 AC2 5 GOL D 704 SITE 1 AC3 5 A C 119 A C 120 C C 122 A C 123 SITE 2 AC3 5 MG C 415 SITE 1 AC4 3 A C 123 G C 143 U C 144 SITE 1 AC5 3 G D 313 A D 320 C D 322 SITE 1 AC6 3 U C 115 U C 116 A D 336 SITE 1 AC7 1 G C 113 SITE 1 AC8 3 A C 104 G C 106 HOH C 806 SITE 1 AC9 1 HOH D 811 SITE 1 BC1 4 A D 307 A D 336 G D 337 HOH D 810 SITE 1 BC2 3 U D 308 U D 310 HOH D 809 SITE 1 BC3 1 G D 306 SITE 1 BC4 3 A C 120 C C 122 K C 404 SITE 1 BC5 1 G C 121 SITE 1 BC6 2 U D 308 A D 311 SITE 1 BC7 1 U C 110 SITE 1 BC8 5 G C 106 A C 107 A C 136 G C 137 SITE 2 BC8 5 HOH C 807 SITE 1 BC9 2 G D 313 A D 320 SITE 1 CC1 8 A D 319 C D 322 A D 323 G D 343 SITE 2 CC1 8 U D 344 A D 346 U D 347 K D 403 SITE 1 CC2 4 GTP C 101 G C 157 GTP D 301 U D 358 CRYST1 150.240 150.240 62.984 90.00 90.00 90.00 P 43 21 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 0.006656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015877 0.00000 HETATM 1 PG GTP C 101 88.690 121.287 11.889 0.50 93.25 P HETATM 2 O1G GTP C 101 90.149 121.802 12.032 0.50 92.62 O HETATM 3 O2G GTP C 101 87.684 122.473 11.886 0.50 93.01 O HETATM 4 O3G GTP C 101 88.498 120.545 10.551 0.50 93.01 O HETATM 5 O3B GTP C 101 88.424 120.219 13.164 1.00 93.19 O HETATM 6 PB GTP C 101 88.993 118.679 13.402 1.00 93.07 P HETATM 7 O1B GTP C 101 87.921 117.689 13.331 1.00 92.33 O HETATM 8 O2B GTP C 101 90.140 118.543 12.398 1.00 93.37 O HETATM 9 O3A GTP C 101 89.609 118.647 14.855 1.00 92.24 O HETATM 10 PA GTP C 101 91.004 118.979 15.521 1.00 91.43 P HETATM 11 O1A GTP C 101 91.309 117.943 16.556 1.00 91.52 O HETATM 12 O2A GTP C 101 92.033 119.339 14.548 1.00 90.79 O HETATM 13 O5' GTP C 101 90.693 119.794 16.574 1.00 71.26 O HETATM 14 C5' GTP C 101 91.641 120.748 17.027 1.00 68.59 C HETATM 15 C4' GTP C 101 91.070 121.421 18.270 1.00 67.96 C HETATM 16 O4' GTP C 101 89.680 121.812 18.039 1.00 67.96 O HETATM 17 C3' GTP C 101 91.077 120.560 19.410 1.00 67.94 C HETATM 18 O3' GTP C 101 92.272 120.192 19.711 1.00 66.64 O HETATM 19 C2' GTP C 101 89.857 121.050 20.278 1.00 67.62 C HETATM 20 O2' GTP C 101 90.307 122.123 21.089 1.00 69.17 O HETATM 21 C1' GTP C 101 88.901 121.557 19.213 1.00 67.34 C HETATM 22 N9 GTP C 101 87.848 120.582 18.888 1.00 66.56 N HETATM 23 C8 GTP C 101 87.656 119.906 17.687 1.00 66.21 C HETATM 24 N7 GTP C 101 86.764 118.939 17.770 1.00 66.03 N HETATM 25 C5 GTP C 101 86.230 119.083 19.046 1.00 65.80 C HETATM 26 C6 GTP C 101 85.201 118.384 19.721 1.00 65.40 C HETATM 27 O6 GTP C 101 84.555 117.456 19.298 1.00 65.76 O HETATM 28 N1 GTP C 101 84.930 118.899 21.000 1.00 65.72 N HETATM 29 C2 GTP C 101 85.594 119.970 21.584 1.00 66.37 C HETATM 30 N2 GTP C 101 85.212 120.321 22.783 1.00 67.29 N HETATM 31 N3 GTP C 101 86.578 120.625 20.986 1.00 65.96 N HETATM 32 C4 GTP C 101 86.864 120.143 19.734 1.00 66.06 C