HEADER TRANSCRIPTION/RNA 29-JUL-04 1U63 TITLE THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-MRNA COMPLEX CAVEAT 1U63 CHIRALITY ERRORS AT RESIDUE 20 B AND 11,12,43 D COMPND MOL_ID: 1; COMPND 2 MOLECULE: 49 NT FRAGMENT OF MRNA FOR L1; COMPND 3 CHAIN: B, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 50S RIBOSOMAL PROTEIN L1P; COMPND 7 CHAIN: A, C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIS OF THE RNA FRAGMENT FROM THE PLASMID PUC18, SOURCE 4 SEQUENCE FROM CELL-FREE(IN VITRO) SYSTEM WITHOUT LIVING ORGANISM; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 7 ORGANISM_TAXID: 2190; SOURCE 8 GENE: RPL1P; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS RIBOSOME, RIBOSOMAL PROTEIN, MRNA-PROTEIN COMPLEX, TRANSCRIPTION-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.NEVSKAYA,S.TISHCHENKO,A.GABDOULKHAKOV,E.NIKONOVA,O.NIKONOV, AUTHOR 2 A.NIKULIN,M.GARBER,S.NIKONOV,W.PIENDL REVDAT 3 30-NOV-16 1U63 1 REMARK VERSN REVDAT 2 24-FEB-09 1U63 1 VERSN REVDAT 1 12-APR-05 1U63 0 JRNL AUTH N.NEVSKAYA,S.TISHCHENKO,A.GABDOULKHAKOV,E.NIKONOVA, JRNL AUTH 2 O.NIKONOV,A.NIKULIN,O.PLATONOVA,M.GARBER,S.NIKONOV,W.PIENDL JRNL TITL RIBOSOMAL PROTEIN L1 RECOGNIZES THE SAME SPECIFIC STRUCTURAL JRNL TITL 2 MOTIF IN ITS TARGET SITES ON THE AUTOREGULATORY MRNA AND 23S JRNL TITL 3 RRNA. JRNL REF NUCLEIC ACIDS RES. V. 33 478 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15659579 JRNL DOI 10.1093/NAR/GKI194 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3657274.330 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 16760 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) : 0.276 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 941 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2646 REMARK 3 BIN R VALUE (WORKING SET) : 0.3940 REMARK 3 BIN FREE R VALUE : 0.4480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 133 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3400 REMARK 3 NUCLEIC ACID ATOMS : 2110 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.40 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) : 0.54 REMARK 3 ESD FROM SIGMAA (A) : 0.88 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) : 0.62 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.98 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 2.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.100 REMARK 3 IMPROPER ANGLES (DEGREES) : 4.070 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) : 16.090; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 25.320; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 16.070; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 20.840; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.19 REMARK 3 BSOL : 36.72 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1U63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-04. REMARK 100 THE RCSB ID CODE IS RCSB023291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97895, 1.05 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17645 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 1.901 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 9.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.84 REMARK 200 R MERGE FOR SHELL (I) : 0.43500 REMARK 200 R SYM FOR SHELL (I) : 0.31800 REMARK 200 FOR SHELL : 2.790 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 10000, MPD, KCL, NACL, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 106.14500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 106.14500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 LYS A 215 REMARK 465 ALA A 216 REMARK 465 LYS A 217 REMARK 465 LYS A 218 REMARK 465 LYS A 219 REMARK 465 LYS C 215 REMARK 465 ALA C 216 REMARK 465 LYS C 217 REMARK 465 LYS C 218 REMARK 465 LYS C 219 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G B 1 P G B 1 OP3 -0.083 REMARK 500 G D 1 P G D 1 OP3 -0.081 REMARK 500 REMARK 500 REMARK: NULL 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 G B 1 O5' - P - OP1 ANGL. DEV. = -6.7 DEGREES REMARK 500 G B 1 O5' - P - OP2 ANGL. DEV. = 16.0 DEGREES REMARK 500 A B 8 O5' - P - OP2 ANGL. DEV. = -16.6 DEGREES REMARK 500 A B 12 N9 - C1' - C2' ANGL. DEV. = 8.3 DEGREES REMARK 500 C B 17 O5' - P - OP2 ANGL. DEV. = -7.7 DEGREES REMARK 500 G B 20 C5' - C4' - O4' ANGL. DEV. = 11.4 DEGREES REMARK 500 G B 20 C2' - C3' - O3' ANGL. DEV. = 14.4 DEGREES REMARK 500 G B 20 N9 - C1' - C2' ANGL. DEV. = 29.7 DEGREES REMARK 500 G B 20 O4' - C1' - N9 ANGL. DEV. = -10.8 DEGREES REMARK 500 A B 21 O3' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 A B 44 N9 - C1' - C2' ANGL. DEV. = 13.1 DEGREES REMARK 500 G D 10 O5' - P - OP1 ANGL. DEV. = -7.5 DEGREES REMARK 500 G D 11 O5' - P - OP2 ANGL. DEV. = -5.9 DEGREES REMARK 500 G D 11 C5' - C4' - O4' ANGL. DEV. = 12.9 DEGREES REMARK 500 G D 11 C2' - C3' - O3' ANGL. DEV. = 13.3 DEGREES REMARK 500 G D 11 N9 - C1' - C2' ANGL. DEV. = 25.3 DEGREES REMARK 500 G D 11 O4' - C1' - N9 ANGL. DEV. = -9.6 DEGREES REMARK 500 G D 11 O3' - P - OP2 ANGL. DEV. = 10.3 DEGREES REMARK 500 A D 12 C5' - C4' - O4' ANGL. DEV. = 6.5 DEGREES REMARK 500 A D 12 C2' - C3' - O3' ANGL. DEV. = 14.4 DEGREES REMARK 500 A D 12 N9 - C1' - C2' ANGL. DEV. = 19.5 DEGREES REMARK 500 A D 12 C8 - N9 - C1' ANGL. DEV. = -17.7 DEGREES REMARK 500 A D 12 C4 - N9 - C1' ANGL. DEV. = 16.3 DEGREES REMARK 500 A D 12 O3' - P - OP2 ANGL. DEV. = 10.5 DEGREES REMARK 500 G D 13 O3' - P - OP2 ANGL. DEV. = 10.3 DEGREES REMARK 500 A D 37 O3' - P - OP1 ANGL. DEV. = 7.1 DEGREES REMARK 500 C D 43 C5' - C4' - O4' ANGL. DEV. = 15.4 DEGREES REMARK 500 C D 43 C2' - C3' - O3' ANGL. DEV. = 14.1 DEGREES REMARK 500 C D 43 N1 - C1' - C2' ANGL. DEV. = 27.6 DEGREES REMARK 500 C D 43 O4' - C1' - N1 ANGL. DEV. = -13.3 DEGREES REMARK 500 A D 44 O3' - P - OP2 ANGL. DEV. = 9.7 DEGREES REMARK 500 PRO A 51 C - N - CA ANGL. DEV. = 9.0 DEGREES REMARK 500 PRO A 207 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 LYS A 212 N - CA - C ANGL. DEV. = 17.8 DEGREES REMARK 500 GLY C 192 N - CA - C ANGL. DEV. = 18.5 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 ALA A 5 -76.23 -57.63 REMARK 500 ASN A 21 37.66 -84.40 REMARK 500 PHE A 22 -170.55 174.45 REMARK 500 LEU A 32 -176.74 -59.93 REMARK 500 LYS A 33 -138.24 -127.39 REMARK 500 ILE A 35 -147.61 -159.30 REMARK 500 ASP A 36 -13.16 -150.43 REMARK 500 MSE A 37 -4.22 55.36 REMARK 500 GLU A 41 132.08 -38.88 REMARK 500 ASN A 42 128.03 -19.90 REMARK 500 ILE A 44 95.23 59.33 REMARK 500 ALA A 58 170.85 -53.17 REMARK 500 ALA A 72 -80.05 -51.84 REMARK 500 LYS A 82 -85.55 -14.21 REMARK 500 ASN A 91 62.20 -166.06 REMARK 500 GLN A 108 84.50 -64.96 REMARK 500 ALA A 109 -63.20 -13.88 REMARK 500 ASP A 110 10.91 -59.31 REMARK 500 PRO A 113 3.33 -49.53 REMARK 500 VAL A 121 -88.40 -23.41 REMARK 500 ILE A 122 29.52 -63.73 REMARK 500 LEU A 123 -58.09 -131.91 REMARK 500 PRO A 125 48.99 -73.79 REMARK 500 ARG A 126 7.40 -150.87 REMARK 500 ALA A 135 -88.87 -1.32 REMARK 500 LEU A 142 -65.34 -96.58 REMARK 500 LYS A 147 -12.64 -46.50 REMARK 500 THR A 154 -2.37 -142.68 REMARK 500 ARG A 155 -150.76 60.87 REMARK 500 VAL A 164 16.46 -158.35 REMARK 500 GLU A 167 -32.77 -35.71 REMARK 500 ASP A 171 -83.63 -14.69 REMARK 500 VAL A 175 -78.44 -28.02 REMARK 500 LYS A 188 -87.96 -36.34 REMARK 500 TYR A 189 -93.02 -123.19 REMARK 500 LEU A 193 -8.51 -169.14 REMARK 500 HIS A 195 21.51 -68.14 REMARK 500 LYS A 197 -73.35 -71.69 REMARK 500 ALA A 208 98.82 -64.58 REMARK 500 LYS A 213 -144.61 -84.51 REMARK 500 ALA C 13 -38.81 -35.60 REMARK 500 LEU C 32 -164.41 -111.74 REMARK 500 LYS C 33 142.24 174.75 REMARK 500 ARG C 43 102.78 -166.02 REMARK 500 ILE C 44 138.86 -32.55 REMARK 500 LYS C 45 108.12 -172.98 REMARK 500 VAL C 49 146.57 -32.60 REMARK 500 ARG C 54 -145.96 -117.89 REMARK 500 ALA C 58 146.56 -33.36 REMARK 500 GLN C 71 -68.67 -26.38 REMARK 500 REMARK 500 THIS ENTRY HAS 80 RAMACHANDRAN OUTLIERS. 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 G B 20 0.15 SIDE CHAIN REMARK 500 A B 44 0.06 SIDE CHAIN REMARK 500 G D 11 0.11 SIDE CHAIN REMARK 500 A D 12 0.05 SIDE CHAIN REMARK 500 C D 43 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 G B 20 18.7 D L WRONG HAND REMARK 500 A B 44 -21.8 D D OUTSIDE RANGE REMARK 500 G D 11 21.1 D L WRONG HAND REMARK 500 A D 12 19.2 D L WRONG HAND REMARK 500 C D 43 22.1 D L WRONG HAND REMARK 500 LYS A 187 23.9 L L OUTSIDE RANGE REMARK 500 LYS A 212 22.6 L L OUTSIDE RANGE REMARK 500 GLU C 167 24.2 L L OUTSIDE RANGE REMARK 500 THR C 170 24.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MZP RELATED DB: PDB REMARK 900 STRUCTURE OF THE L1 PROTUBERANCE IN THE RIBOSOME REMARK 900 RELATED ID: 1AD2 RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L1 FROM THERMUS THERMOPHILUS REMARK 900 RELATED ID: 1CSJ RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS JANNASCHII REMARK 900 RELATED ID: 1DWU RELATED DB: PDB REMARK 900 RIBOSOMAL PROTEIN L1 FROM METHANOCOCCUS THERMOLITHOTROPHICUS DBREF 1U63 A 1 219 UNP P54050 RL1_METJA 1 219 DBREF 1U63 C 1 219 UNP P54050 RL1_METJA 1 219 DBREF 1U63 B 1 49 PDB 1U63 1U63 1 49 DBREF 1U63 D 1 49 PDB 1U63 1U63 1 49 SEQADV 1U63 MSE A 37 UNP P54050 MET 37 MODIFIED RESIDUE SEQADV 1U63 MSE A 112 UNP P54050 MET 112 MODIFIED RESIDUE SEQADV 1U63 MSE A 119 UNP P54050 MET 119 MODIFIED RESIDUE SEQADV 1U63 MSE A 129 UNP P54050 MET 129 MODIFIED RESIDUE SEQADV 1U63 MSE A 169 UNP P54050 MET 169 MODIFIED RESIDUE SEQADV 1U63 MSE A 205 UNP P54050 MET 205 MODIFIED RESIDUE SEQADV 1U63 MSE C 37 UNP P54050 MET 37 MODIFIED RESIDUE SEQADV 1U63 MSE C 112 UNP P54050 MET 112 MODIFIED RESIDUE SEQADV 1U63 MSE C 119 UNP P54050 MET 119 MODIFIED RESIDUE SEQADV 1U63 MSE C 129 UNP P54050 MET 129 MODIFIED RESIDUE SEQADV 1U63 MSE C 169 UNP P54050 MET 169 MODIFIED RESIDUE SEQADV 1U63 MSE C 205 UNP P54050 MET 205 MODIFIED RESIDUE SEQRES 1 B 49 G G G A G U G A A G G A G SEQRES 2 B 49 G C U C G C G A A C U C G SEQRES 3 B 49 C G A A G C C G A G A A A SEQRES 4 B 49 C U U C A C U C C C SEQRES 1 D 49 G G G A G U G A A G G A G SEQRES 2 D 49 G C U C G C G A A C U C G SEQRES 3 D 49 C G A A G C C G A G A A A SEQRES 4 D 49 C U U C A C U C C C SEQRES 1 A 219 MET ASP ARG GLU ALA LEU LEU GLN ALA VAL LYS GLU ALA SEQRES 2 A 219 ARG GLU LEU ALA LYS PRO ARG ASN PHE THR GLN SER PHE SEQRES 3 A 219 GLU PHE ILE ALA THR LEU LYS GLU ILE ASP MSE ARG LYS SEQRES 4 A 219 PRO GLU ASN ARG ILE LYS THR GLU VAL VAL LEU PRO HIS SEQRES 5 A 219 GLY ARG GLY LYS GLU ALA LYS ILE ALA VAL ILE GLY THR SEQRES 6 A 219 GLY ASP LEU ALA LYS GLN ALA GLU GLU LEU GLY LEU THR SEQRES 7 A 219 VAL ILE ARG LYS GLU GLU ILE GLU GLU LEU GLY LYS ASN SEQRES 8 A 219 LYS ARG LYS LEU ARG LYS ILE ALA LYS ALA HIS ASP PHE SEQRES 9 A 219 PHE ILE ALA GLN ALA ASP LEU MSE PRO LEU ILE GLY ARG SEQRES 10 A 219 TYR MSE GLY VAL ILE LEU GLY PRO ARG GLY LYS MSE PRO SEQRES 11 A 219 LYS PRO VAL PRO ALA ASN ALA ASN ILE LYS PRO LEU VAL SEQRES 12 A 219 GLU ARG LEU LYS LYS THR VAL VAL ILE ASN THR ARG ASP SEQRES 13 A 219 LYS PRO TYR PHE GLN VAL LEU VAL GLY ASN GLU LYS MSE SEQRES 14 A 219 THR ASP GLU GLN ILE VAL ASP ASN ILE GLU ALA VAL LEU SEQRES 15 A 219 ASN VAL VAL ALA LYS LYS TYR GLU LYS GLY LEU TYR HIS SEQRES 16 A 219 ILE LYS ASP ALA TYR VAL LYS LEU THR MSE GLY PRO ALA SEQRES 17 A 219 VAL LYS VAL LYS LYS GLU LYS ALA LYS LYS LYS SEQRES 1 C 219 MET ASP ARG GLU ALA LEU LEU GLN ALA VAL LYS GLU ALA SEQRES 2 C 219 ARG GLU LEU ALA LYS PRO ARG ASN PHE THR GLN SER PHE SEQRES 3 C 219 GLU PHE ILE ALA THR LEU LYS GLU ILE ASP MSE ARG LYS SEQRES 4 C 219 PRO GLU ASN ARG ILE LYS THR GLU VAL VAL LEU PRO HIS SEQRES 5 C 219 GLY ARG GLY LYS GLU ALA LYS ILE ALA VAL ILE GLY THR SEQRES 6 C 219 GLY ASP LEU ALA LYS GLN ALA GLU GLU LEU GLY LEU THR SEQRES 7 C 219 VAL ILE ARG LYS GLU GLU ILE GLU GLU LEU GLY LYS ASN SEQRES 8 C 219 LYS ARG LYS LEU ARG LYS ILE ALA LYS ALA HIS ASP PHE SEQRES 9 C 219 PHE ILE ALA GLN ALA ASP LEU MSE PRO LEU ILE GLY ARG SEQRES 10 C 219 TYR MSE GLY VAL ILE LEU GLY PRO ARG GLY LYS MSE PRO SEQRES 11 C 219 LYS PRO VAL PRO ALA ASN ALA ASN ILE LYS PRO LEU VAL SEQRES 12 C 219 GLU ARG LEU LYS LYS THR VAL VAL ILE ASN THR ARG ASP SEQRES 13 C 219 LYS PRO TYR PHE GLN VAL LEU VAL GLY ASN GLU LYS MSE SEQRES 14 C 219 THR ASP GLU GLN ILE VAL ASP ASN ILE GLU ALA VAL LEU SEQRES 15 C 219 ASN VAL VAL ALA LYS LYS TYR GLU LYS GLY LEU TYR HIS SEQRES 16 C 219 ILE LYS ASP ALA TYR VAL LYS LEU THR MSE GLY PRO ALA SEQRES 17 C 219 VAL LYS VAL LYS LYS GLU LYS ALA LYS LYS LYS MODRES 1U63 MSE A 37 MET SELENOMETHIONINE MODRES 1U63 MSE A 112 MET SELENOMETHIONINE MODRES 1U63 MSE A 119 MET SELENOMETHIONINE MODRES 1U63 MSE A 129 MET SELENOMETHIONINE MODRES 1U63 MSE A 169 MET SELENOMETHIONINE MODRES 1U63 MSE A 205 MET SELENOMETHIONINE MODRES 1U63 MSE C 37 MET SELENOMETHIONINE MODRES 1U63 MSE C 112 MET SELENOMETHIONINE MODRES 1U63 MSE C 119 MET SELENOMETHIONINE MODRES 1U63 MSE C 129 MET SELENOMETHIONINE MODRES 1U63 MSE C 169 MET SELENOMETHIONINE MODRES 1U63 MSE C 205 MET SELENOMETHIONINE HET MSE A 37 8 HET MSE A 112 8 HET MSE A 119 8 HET MSE A 129 8 HET MSE A 169 8 HET MSE A 205 8 HET MSE C 37 8 HET MSE C 112 8 HET MSE C 119 8 HET MSE C 129 8 HET MSE C 169 8 HET MSE C 205 8 HETNAM MSE SELENOMETHIONINE FORMUL 3 MSE 12(C5 H11 N O2 SE) HELIX 1 1 ASP A 2 LEU A 16 1 15 HELIX 2 2 THR A 65 LEU A 75 1 11 HELIX 3 3 LYS A 82 LYS A 90 1 9 HELIX 4 4 ASN A 91 HIS A 102 1 12 HELIX 5 5 LEU A 111 MSE A 119 1 9 HELIX 6 6 LEU A 123 GLY A 127 5 5 HELIX 7 7 ILE A 139 LYS A 147 1 9 HELIX 8 8 THR A 170 LYS A 187 1 18 HELIX 9 9 ASP C 2 ARG C 14 1 13 HELIX 10 10 GLU C 15 ALA C 17 5 3 HELIX 11 11 THR C 65 GLY C 76 1 12 HELIX 12 12 GLU C 83 GLY C 89 1 7 HELIX 13 13 ARG C 93 HIS C 102 1 10 HELIX 14 14 MSE C 112 ARG C 117 1 6 HELIX 15 15 LEU C 123 GLY C 127 5 5 HELIX 16 16 ILE C 139 LYS C 147 1 9 HELIX 17 17 THR C 170 LYS C 187 1 18 SHEET 1 A 3 TYR A 159 LEU A 163 0 SHEET 2 A 3 PHE A 26 THR A 31 -1 N ALA A 30 O PHE A 160 SHEET 3 A 3 ALA A 199 LEU A 203 -1 O LYS A 202 N GLU A 27 SHEET 1 B 2 GLU A 47 VAL A 49 0 SHEET 2 B 2 THR A 149 VAL A 151 -1 O VAL A 150 N VAL A 48 SHEET 1 C 4 THR A 78 ARG A 81 0 SHEET 2 C 4 ILE A 60 GLY A 64 1 N VAL A 62 O ILE A 80 SHEET 3 C 4 PHE A 104 GLN A 108 1 O ILE A 106 N ILE A 63 SHEET 4 C 4 LYS A 131 VAL A 133 1 O LYS A 131 N PHE A 105 SHEET 1 D 4 TYR C 159 ASN C 166 0 SHEET 2 D 4 SER C 25 THR C 31 -1 N PHE C 28 O VAL C 162 SHEET 3 D 4 ALA C 199 LEU C 203 -1 O TYR C 200 N ILE C 29 SHEET 4 D 4 VAL C 209 LYS C 210 -1 O VAL C 209 N VAL C 201 SHEET 1 E 2 LYS C 45 GLU C 47 0 SHEET 2 E 2 VAL C 151 ASN C 153 -1 O ILE C 152 N THR C 46 SHEET 1 F 4 THR C 78 ILE C 80 0 SHEET 2 F 4 ILE C 60 ILE C 63 1 N VAL C 62 O THR C 78 SHEET 3 F 4 PHE C 104 GLN C 108 1 O GLN C 108 N ILE C 63 SHEET 4 F 4 LYS C 131 VAL C 133 1 O LYS C 131 N PHE C 105 LINK C ASP A 36 N MSE A 37 1555 1555 1.33 LINK C MSE A 37 N ARG A 38 1555 1555 1.33 LINK C LEU A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N PRO A 113 1555 1555 1.34 LINK C TYR A 118 N MSE A 119 1555 1555 1.33 LINK C MSE A 119 N GLY A 120 1555 1555 1.33 LINK C LYS A 128 N MSE A 129 1555 1555 1.33 LINK C MSE A 129 N PRO A 130 1555 1555 1.34 LINK C LYS A 168 N MSE A 169 1555 1555 1.33 LINK C MSE A 169 N THR A 170 1555 1555 1.33 LINK C THR A 204 N MSE A 205 1555 1555 1.33 LINK C MSE A 205 N GLY A 206 1555 1555 1.33 LINK C ASP C 36 N MSE C 37 1555 1555 1.33 LINK C MSE C 37 N ARG C 38 1555 1555 1.33 LINK C LEU C 111 N MSE C 112 1555 1555 1.33 LINK C MSE C 112 N PRO C 113 1555 1555 1.34 LINK C TYR C 118 N MSE C 119 1555 1555 1.33 LINK C MSE C 119 N GLY C 120 1555 1555 1.32 LINK C LYS C 128 N MSE C 129 1555 1555 1.33 LINK C MSE C 129 N PRO C 130 1555 1555 1.33 LINK C LYS C 168 N MSE C 169 1555 1555 1.34 LINK C MSE C 169 N THR C 170 1555 1555 1.33 LINK C THR C 204 N MSE C 205 1555 1555 1.33 LINK C MSE C 205 N GLY C 206 1555 1555 1.33 CRYST1 212.290 68.900 115.870 90.00 122.99 90.00 C 1 2 1 8 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 0.004711 0.000000 0.003058 0.00000 SCALE2 0.000000 0.014514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010289 0.00000