HEADER TRANSFERASE/RNA 17-FEB-06 2DET TITLE COCRYSTAL STRUCTURE OF AN RNA SULFURATION ENZYME MNMA AND TRNA-GLU IN TITLE 2 THE PRE-REACTION STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRNA-SPECIFIC 2-THIOURIDYLASE MNMA; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: RNA SULFURATION ENZYME MNMA; COMPND 9 EC: 2.8.1.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION.; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 6 ORGANISM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE80L KEYWDS PROTEIN-RNA COMPLEX, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.NUMATA,Y.IKEUCHI,S.FUKAI,T.SUZUKI,O.NUREKI REVDAT 3 13-NOV-24 2DET 1 REMARK SEQADV REVDAT 2 13-JAN-09 2DET 1 COMPND VERSN REVDAT 1 15-AUG-06 2DET 0 JRNL AUTH T.NUMATA,Y.IKEUCHI,S.FUKAI,T.SUZUKI,O.NUREKI JRNL TITL SNAPSHOTS OF TRNA SULPHURATION VIA AN ADENYLATED JRNL TITL 2 INTERMEDIATE JRNL REF NATURE V. 442 419 2006 JRNL REFN ISSN 0028-0836 JRNL PMID 16871210 JRNL DOI 10.1038/NATURE04896 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) : 39.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 203041.500 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 15834 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) : 0.263 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 758 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 3.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2443 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2861 REMARK 3 NUCLEIC ACID ATOMS : 1488 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 0.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.05000 REMARK 3 B22 (A**2) : -17.52000 REMARK 3 B33 (A**2) : 7.46000 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.62 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) : 0.54 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.86 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.12 REMARK 3 BSOL : 10.00 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-05; 04-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL41XU; BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97904, 0.97931, 0.9760, REMARK 200 0.9820; 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28072 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.4000 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) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES-NA BUFFER (PH 7.5), 1.3 REMARK 280 -1.5M LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-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 50.76850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.61950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.00750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 105.61950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.76850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.00750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 50.76850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.00750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 105.61950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.00750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 50.76850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 105.61950 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: 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 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 A C 71 REMARK 465 C C 72 REMARK 465 G C 73 REMARK 465 C C 74 REMARK 465 C C 75 REMARK 465 A C 76 REMARK 465 MET A -11 REMARK 465 ARG A -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 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 C 1 P G C 1 OP3 -0.086 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 C 18 N9 - C1' - C2' ANGL. DEV. = 8.1 DEGREES REMARK 500 C C 47 N1 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 CYS A 199 CA - CB - SG ANGL. DEV. = 9.6 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 ASP A 17 -75.06 -39.53 REMARK 500 SER A 19 -88.51 -27.00 REMARK 500 TYR A 30 134.35 -14.06 REMARK 500 GLU A 41 87.21 -68.14 REMARK 500 GLU A 42 127.62 -19.83 REMARK 500 ASP A 44 -103.06 -120.12 REMARK 500 GLU A 46 -33.67 -39.16 REMARK 500 THR A 50 -70.52 -44.95 REMARK 500 ALA A 51 -61.92 -25.52 REMARK 500 ALA A 58 -76.96 -55.75 REMARK 500 ALA A 60 -36.30 -31.89 REMARK 500 LYS A 64 -3.34 -56.98 REMARK 500 ALA A 75 -36.88 -39.50 REMARK 500 ALA A 76 -76.60 -53.53 REMARK 500 TYR A 78 -76.02 -31.92 REMARK 500 VAL A 82 -79.83 -123.54 REMARK 500 GLU A 84 -65.96 -28.62 REMARK 500 PHE A 86 -31.67 -35.03 REMARK 500 ILE A 100 0.79 -61.15 REMARK 500 ILE A 106 -84.27 -95.54 REMARK 500 LYS A 107 -37.78 -37.22 REMARK 500 LYS A 109 -83.60 -74.24 REMARK 500 PHE A 111 -73.84 -44.60 REMARK 500 GLU A 113 -71.04 -51.89 REMARK 500 PHE A 114 10.84 -57.36 REMARK 500 ASP A 118 -75.57 -124.75 REMARK 500 LEU A 119 -4.36 -58.39 REMARK 500 ASP A 122 -70.13 -93.25 REMARK 500 HIS A 128 119.77 -37.22 REMARK 500 ASP A 136 13.68 56.37 REMARK 500 LEU A 145 163.84 -43.59 REMARK 500 LEU A 155 40.46 -95.60 REMARK 500 HIS A 160 -51.83 -6.92 REMARK 500 VAL A 178 -77.68 -33.82 REMARK 500 ASP A 194 52.81 -58.20 REMARK 500 SER A 195 -138.03 55.48 REMARK 500 THR A 196 151.83 131.73 REMARK 500 ILE A 198 135.35 -27.59 REMARK 500 PHE A 200 -17.28 83.22 REMARK 500 PHE A 206 -77.20 -44.07 REMARK 500 ARG A 207 -58.13 -15.32 REMARK 500 PRO A 218 96.41 -58.50 REMARK 500 ILE A 222 -155.34 -85.88 REMARK 500 ASP A 227 126.26 -172.40 REMARK 500 ILE A 229 -53.98 -163.63 REMARK 500 GLU A 231 -127.77 -68.34 REMARK 500 HIS A 232 -18.88 175.93 REMARK 500 GLN A 233 65.05 12.82 REMARK 500 LEU A 235 -40.99 -156.90 REMARK 500 LEU A 240 133.87 -33.75 REMARK 500 REMARK 500 THIS ENTRY HAS 75 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 C 17 0.06 SIDE CHAIN REMARK 500 C C 20 0.06 SIDE CHAIN REMARK 500 C C 47 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DER RELATED DB: PDB REMARK 900 THE SAME PROTEIN/TRNA COMPLEX IN THE INITIAL TRNA BINDING STATE REMARK 900 RELATED ID: 2DEU RELATED DB: PDB REMARK 900 THE SAME PROTEIN/TRNA COMPLEX IN THE ADENYLATED INTERMEDIATE STATE DBREF 2DET A 1 368 UNP P25745 TRMU_ECOLI 1 368 DBREF 2DET C 1 76 PDB 2DET 2DET 1 76 SEQADV 2DET MET A -11 UNP P25745 EXPRESSION TAG SEQADV 2DET ARG A -10 UNP P25745 EXPRESSION TAG SEQADV 2DET GLY A -9 UNP P25745 EXPRESSION TAG SEQADV 2DET SER A -8 UNP P25745 EXPRESSION TAG SEQADV 2DET HIS A -7 UNP P25745 EXPRESSION TAG SEQADV 2DET HIS A -6 UNP P25745 EXPRESSION TAG SEQADV 2DET HIS A -5 UNP P25745 EXPRESSION TAG SEQADV 2DET HIS A -4 UNP P25745 EXPRESSION TAG SEQADV 2DET HIS A -3 UNP P25745 EXPRESSION TAG SEQADV 2DET HIS A -2 UNP P25745 EXPRESSION TAG SEQADV 2DET GLY A -1 UNP P25745 EXPRESSION TAG SEQADV 2DET SER A 0 UNP P25745 EXPRESSION TAG SEQRES 1 C 76 G U C C C C U U C G U C U SEQRES 2 C 76 A G A G G C C C A G G A C SEQRES 3 C 76 A C C G C C C U U U C A C SEQRES 4 C 76 G G C G G U A A C A G G G SEQRES 5 C 76 G U U C G A A U C C C C U SEQRES 6 C 76 A G G G G A C G C C A SEQRES 1 A 380 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER MET SEQRES 2 A 380 SER GLU THR ALA LYS LYS VAL ILE VAL GLY MET SER GLY SEQRES 3 A 380 GLY VAL ASP SER SER VAL SER ALA TRP LEU LEU GLN GLN SEQRES 4 A 380 GLN GLY TYR GLN VAL GLU GLY LEU PHE MET LYS ASN TRP SEQRES 5 A 380 GLU GLU ASP ASP GLY GLU GLU TYR CYS THR ALA ALA ALA SEQRES 6 A 380 ASP LEU ALA ASP ALA GLN ALA VAL CYS ASP LYS LEU GLY SEQRES 7 A 380 ILE GLU LEU HIS THR VAL ASN PHE ALA ALA GLU TYR TRP SEQRES 8 A 380 ASP ASN VAL PHE GLU LEU PHE LEU ALA GLU TYR LYS ALA SEQRES 9 A 380 GLY ARG THR PRO ASN PRO ASP ILE LEU CYS ASN LYS GLU SEQRES 10 A 380 ILE LYS PHE LYS ALA PHE LEU GLU PHE ALA ALA GLU ASP SEQRES 11 A 380 LEU GLY ALA ASP TYR ILE ALA THR GLY HIS TYR VAL ARG SEQRES 12 A 380 ARG ALA ASP VAL ASP GLY LYS SER ARG LEU LEU ARG GLY SEQRES 13 A 380 LEU ASP SER ASN LYS ASP GLN SER TYR PHE LEU TYR THR SEQRES 14 A 380 LEU SER HIS GLU GLN ILE ALA GLN SER LEU PHE PRO VAL SEQRES 15 A 380 GLY GLU LEU GLU LYS PRO GLN VAL ARG LYS ILE ALA GLU SEQRES 16 A 380 ASP LEU GLY LEU VAL THR ALA LYS LYS LYS ASP SER THR SEQRES 17 A 380 GLY ILE CYS PHE ILE GLY GLU ARG LYS PHE ARG GLU PHE SEQRES 18 A 380 LEU GLY ARG TYR LEU PRO ALA GLN PRO GLY LYS ILE ILE SEQRES 19 A 380 THR VAL ASP GLY ASP GLU ILE GLY GLU HIS GLN GLY LEU SEQRES 20 A 380 MET TYR HIS THR LEU GLY GLN ARG LYS GLY LEU GLY ILE SEQRES 21 A 380 GLY GLY THR LYS GLU GLY THR GLU GLU PRO TRP TYR VAL SEQRES 22 A 380 VAL ASP LYS ASP VAL GLU ASN ASN ILE LEU VAL VAL ALA SEQRES 23 A 380 GLN GLY HIS GLU HIS PRO ARG LEU MET SER VAL GLY LEU SEQRES 24 A 380 ILE ALA GLN GLN LEU HIS TRP VAL ASP ARG GLU PRO PHE SEQRES 25 A 380 THR GLY THR MET ARG CYS THR VAL LYS THR ARG TYR ARG SEQRES 26 A 380 GLN THR ASP ILE PRO CYS THR VAL LYS ALA LEU ASP ASP SEQRES 27 A 380 ASP ARG ILE GLU VAL ILE PHE ASP GLU PRO VAL ALA ALA SEQRES 28 A 380 VAL THR PRO GLY GLN SER ALA VAL PHE TYR ASN GLY GLU SEQRES 29 A 380 VAL CYS LEU GLY GLY GLY ILE ILE GLU GLN ARG LEU PRO SEQRES 30 A 380 LEU PRO VAL HET SO4 A5001 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- HELIX 1 1 GLY A 15 GLY A 29 1 15 HELIX 2 2 GLY A 45 GLY A 66 1 22 HELIX 3 3 PHE A 74 VAL A 82 1 9 HELIX 4 4 VAL A 82 ALA A 92 1 11 HELIX 5 5 PRO A 98 ILE A 106 1 9 HELIX 6 6 LYS A 109 GLU A 117 1 9 HELIX 7 7 ASP A 146 ASP A 150 5 5 HELIX 8 8 GLN A 151 THR A 157 5 7 HELIX 9 9 HIS A 160 GLN A 165 1 6 HELIX 10 10 PRO A 169 LEU A 173 5 5 HELIX 11 11 GLU A 174 GLY A 186 1 13 HELIX 12 12 LYS A 205 GLY A 211 1 7 HELIX 13 13 HIS A 279 ARG A 281 5 3 SHEET 1 A 4 GLN A 31 LEU A 35 0 SHEET 2 A 4 LYS A 7 GLY A 11 1 N VAL A 8 O GLN A 31 SHEET 3 A 4 TYR A 123 ALA A 125 1 O ALA A 125 N GLY A 11 SHEET 4 A 4 SER A 166 LEU A 167 1 O LEU A 167 N ILE A 124 SHEET 1 B 2 ARG A 131 VAL A 135 0 SHEET 2 B 2 LYS A 138 LEU A 142 -1 O LEU A 142 N ARG A 131 SHEET 1 C 2 TRP A 259 ASP A 263 0 SHEET 2 C 2 VAL A 272 GLN A 275 -1 O ALA A 274 N TYR A 260 SHEET 1 D 7 MET A 283 GLN A 290 0 SHEET 2 D 7 ILE A 329 ALA A 338 -1 O VAL A 331 N LEU A 287 SHEET 3 D 7 ILE A 317 LYS A 322 -1 N PRO A 318 O ASP A 334 SHEET 4 D 7 THR A 303 LYS A 309 -1 N CYS A 306 O CYS A 319 SHEET 5 D 7 SER A 345 ASN A 350 -1 O VAL A 347 N LYS A 309 SHEET 6 D 7 VAL A 353 PRO A 365 -1 O GLY A 358 N ALA A 346 SHEET 7 D 7 MET A 283 GLN A 290 -1 N VAL A 285 O LEU A 364 SSBOND 1 CYS A 102 CYS A 199 1555 1555 2.05 SITE 1 AC1 5 SER A 13 GLY A 14 GLY A 15 ASP A 17 SITE 2 AC1 5 SER A 18 CRYST1 101.537 108.015 211.239 90.00 90.00 90.00 I 21 21 21 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 0.009849 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004734 0.00000