HEADER TRANSFERASE/RNA 07-JAN-09 2ZXU TITLE CRYSTAL STRUCTURE OF TRNA MODIFICATION ENZYME MIAA IN THE COMPLEX WITH TITLE 2 TRNA(PHE) AND DMASPP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MIAA, IPP TRANSFERASE, ISOPENTENYL-DIPHOSPHATE:TRNA COMPND 5 ISOPENTENYLTRANSFERASE, IPTASE, IPPT; COMPND 6 EC: 2.5.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRNA(PHE); COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: MINAA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 14 ORGANISM_TAXID: 83333; SOURCE 15 OTHER_DETAILS: TRNA(PHE) WAS PREPARED BY IN VITRO TRANSCRIPTION. SOURCE 16 THIS SEQUENCE OCCURS NATURALLY IN ESCHERICHIA COLI ST.K12. KEYWDS PROTEIN-RNA COMPLEX, ATP-BINDING, TRNA MODIFICATION ENZYME, KEYWDS 2 NUCLEOTIDE-BINDING, NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRNA KEYWDS 3 PROCESSING, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.SAKAI,M.YAO,S.CHIMNARONK,I.TANAKA REVDAT 4 01-NOV-23 2ZXU 1 REMARK HETSYN LINK REVDAT 3 16-OCT-19 2ZXU 1 COMPND FORMUL REVDAT 2 16-JUN-09 2ZXU 1 JRNL REVDAT 1 26-MAY-09 2ZXU 0 JRNL AUTH S.CHIMNARONK,F.FOROUHAR,J.SAKAI,M.YAO,C.M.TRON,M.ATTA, JRNL AUTH 2 M.FONTECAVE,J.F.HUNT,I.TANAKA JRNL TITL SNAPSHOTS OF DYNAMICS IN SYNTHESIZING JRNL TITL 2 N(6)-ISOPENTENYLADENOSINE AT THE TRNA ANTICODON JRNL REF BIOCHEMISTRY V. 48 5057 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19435325 JRNL DOI 10.1021/BI900337D REMARK 2 REMARK 2 RESOLUTION. 2.75 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31721 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) : 0.237 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2211 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2900 REMARK 3 BIN R VALUE (WORKING SET) : 0.3169 REMARK 3 BIN FREE R VALUE : 0.3645 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 236 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 : 4800 REMARK 3 NUCLEIC ACID ATOMS : 3046 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.24700 REMARK 3 B22 (A**2) : -9.80000 REMARK 3 B33 (A**2) : 8.55400 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.330 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.22 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.470 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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: LAFIRE WAS ALSO USED IN REFINEMENT. REMARK 4 REMARK 4 2ZXU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000028561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 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) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : 0.36800 REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: LAFIRE REMARK 200 STARTING MODEL: PDB ENTRY 2ZM5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09M MES, 24% PEG 3350, 0.18MM REMARK 280 CA(OAC)2, 0.01MM TRI-SODIUM CITRATE DIHYDRATE PH 5.6, 2% ISO- REMARK 280 PROPANOL, 2% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K, PH 5.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 44.15000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.00000 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, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -149.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 ILE A 4 REMARK 465 SER A 5 REMARK 465 LYS A 6 REMARK 465 ALA A 7 REMARK 465 SER A 8 REMARK 465 ALA A 315 REMARK 465 GLY A 316 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASP B 3 REMARK 465 ILE B 4 REMARK 465 SER B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 312 REMARK 465 ALA B 313 REMARK 465 ILE B 314 REMARK 465 ALA B 315 REMARK 465 GLY B 316 REMARK 465 C C 75 REMARK 465 A C 76 REMARK 465 G D 70 REMARK 465 G D 71 REMARK 465 C D 72 REMARK 465 A D 73 REMARK 465 C D 74 REMARK 465 C D 75 REMARK 465 A D 76 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP1 U C 20 O HOH C 111 2.11 REMARK 500 O2' G C 18 N2 G C 57 2.13 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 ARG B 217 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 G C 18 N9 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 G C 19 N9 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 G D 34 N9 - C1' - C2' ANGL. DEV. = 8.7 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 VAL A 41 77.77 -119.99 REMARK 500 PRO A 75 -11.35 -48.57 REMARK 500 PRO A 194 50.55 -68.88 REMARK 500 GLU A 298 177.41 -51.07 REMARK 500 LYS A 299 -30.25 -25.27 REMARK 500 PRO A 300 33.57 -63.12 REMARK 500 GLN A 302 48.02 -74.92 REMARK 500 ALA B 20 30.48 74.32 REMARK 500 PRO B 75 -11.91 -48.22 REMARK 500 ALA B 97 -7.54 -57.65 REMARK 500 ILE B 133 -7.00 -49.55 REMARK 500 GLN B 140 97.13 -24.12 REMARK 500 TRP B 142 13.27 -58.84 REMARK 500 PRO B 194 49.73 -68.90 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 U C 8 0.07 SIDE CHAIN REMARK 500 G C 19 0.07 SIDE CHAIN REMARK 500 G D 22 0.06 SIDE CHAIN REMARK 500 G D 34 0.07 SIDE CHAIN REMARK 500 A D 37 0.07 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 A 318 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 24 OG1 REMARK 620 2 DST A 317 O5 81.9 REMARK 620 3 DST A 317 O7 154.8 73.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 318 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 24 OG1 REMARK 620 2 DST B 317 O5 81.7 REMARK 620 3 DST B 317 O7 156.8 79.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 79 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 7 OP1 REMARK 620 2 U C 8 O4 95.8 REMARK 620 3 HOH C 112 O 155.5 86.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 77 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 17 OP1 REMARK 620 2 G C 19 OP1 97.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 82 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 22 OP2 REMARK 620 2 G C 46 O6 99.9 REMARK 620 3 HOH C 195 O 103.4 72.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 77 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 27 N7 REMARK 620 2 G D 27 O6 86.4 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 DST A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DST B 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 77 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 78 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 79 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 77 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 80 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 81 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 82 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 83 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 318 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZM5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN/TRNA COMPLEX WITHOUT LIGAND DBREF 2ZXU A 1 316 UNP P16384 MIAA_ECOLI 1 316 DBREF 2ZXU B 1 316 UNP P16384 MIAA_ECOLI 1 316 DBREF1 2ZXU C 1 76 GB CP000948 DBREF2 2ZXU C 169887498 3207931 3208006 DBREF1 2ZXU D 1 76 GB CP000948 DBREF2 2ZXU D 169887498 3207931 3208006 SEQRES 1 A 316 MET SER ASP ILE SER LYS ALA SER LEU PRO LYS ALA ILE SEQRES 2 A 316 PHE LEU MET GLY PRO THR ALA SER GLY LYS THR ALA LEU SEQRES 3 A 316 ALA ILE GLU LEU ARG LYS ILE LEU PRO VAL GLU LEU ILE SEQRES 4 A 316 SER VAL ASP SER ALA LEU ILE TYR LYS GLY MET ASP ILE SEQRES 5 A 316 GLY THR ALA LYS PRO ASN ALA GLU GLU LEU LEU ALA ALA SEQRES 6 A 316 PRO HIS ARG LEU LEU ASP ILE ARG ASP PRO SER GLN ALA SEQRES 7 A 316 TYR SER ALA ALA ASP PHE ARG ARG ASP ALA LEU ALA GLU SEQRES 8 A 316 MET ALA ASP ILE THR ALA ALA GLY ARG ILE PRO LEU LEU SEQRES 9 A 316 VAL GLY GLY THR MET LEU TYR PHE LYS ALA LEU LEU GLU SEQRES 10 A 316 GLY LEU SER PRO LEU PRO SER ALA ASP PRO GLU VAL ARG SEQRES 11 A 316 ALA ARG ILE GLU GLN GLN ALA ALA GLU GLN GLY TRP GLU SEQRES 12 A 316 SER LEU HIS ARG GLN LEU GLN GLU VAL ASP PRO VAL ALA SEQRES 13 A 316 ALA ALA ARG ILE HIS PRO ASN ASP PRO GLN ARG LEU SER SEQRES 14 A 316 ARG ALA LEU GLU VAL PHE PHE ILE SER GLY LYS THR LEU SEQRES 15 A 316 THR GLU LEU THR GLN THR SER GLY ASP ALA LEU PRO TYR SEQRES 16 A 316 GLN VAL HIS GLN PHE ALA ILE ALA PRO ALA SER ARG GLU SEQRES 17 A 316 LEU LEU HIS GLN ARG ILE GLU GLN ARG PHE HIS GLN MET SEQRES 18 A 316 LEU ALA SER GLY PHE GLU ALA GLU VAL ARG ALA LEU PHE SEQRES 19 A 316 ALA ARG GLY ASP LEU HIS THR ASP LEU PRO SER ILE ARG SEQRES 20 A 316 CYS VAL GLY TYR ARG GLN MET TRP SER TYR LEU GLU GLY SEQRES 21 A 316 GLU ILE SER TYR ASP GLU MET VAL TYR ARG GLY VAL CYS SEQRES 22 A 316 ALA THR ARG GLN LEU ALA LYS ARG GLN ILE THR TRP LEU SEQRES 23 A 316 ARG GLY TRP GLU GLY VAL HIS TRP LEU ASP SER GLU LYS SEQRES 24 A 316 PRO GLU GLN ALA ARG ASP GLU VAL LEU GLN VAL VAL GLY SEQRES 25 A 316 ALA ILE ALA GLY SEQRES 1 B 316 MET SER ASP ILE SER LYS ALA SER LEU PRO LYS ALA ILE SEQRES 2 B 316 PHE LEU MET GLY PRO THR ALA SER GLY LYS THR ALA LEU SEQRES 3 B 316 ALA ILE GLU LEU ARG LYS ILE LEU PRO VAL GLU LEU ILE SEQRES 4 B 316 SER VAL ASP SER ALA LEU ILE TYR LYS GLY MET ASP ILE SEQRES 5 B 316 GLY THR ALA LYS PRO ASN ALA GLU GLU LEU LEU ALA ALA SEQRES 6 B 316 PRO HIS ARG LEU LEU ASP ILE ARG ASP PRO SER GLN ALA SEQRES 7 B 316 TYR SER ALA ALA ASP PHE ARG ARG ASP ALA LEU ALA GLU SEQRES 8 B 316 MET ALA ASP ILE THR ALA ALA GLY ARG ILE PRO LEU LEU SEQRES 9 B 316 VAL GLY GLY THR MET LEU TYR PHE LYS ALA LEU LEU GLU SEQRES 10 B 316 GLY LEU SER PRO LEU PRO SER ALA ASP PRO GLU VAL ARG SEQRES 11 B 316 ALA ARG ILE GLU GLN GLN ALA ALA GLU GLN GLY TRP GLU SEQRES 12 B 316 SER LEU HIS ARG GLN LEU GLN GLU VAL ASP PRO VAL ALA SEQRES 13 B 316 ALA ALA ARG ILE HIS PRO ASN ASP PRO GLN ARG LEU SER SEQRES 14 B 316 ARG ALA LEU GLU VAL PHE PHE ILE SER GLY LYS THR LEU SEQRES 15 B 316 THR GLU LEU THR GLN THR SER GLY ASP ALA LEU PRO TYR SEQRES 16 B 316 GLN VAL HIS GLN PHE ALA ILE ALA PRO ALA SER ARG GLU SEQRES 17 B 316 LEU LEU HIS GLN ARG ILE GLU GLN ARG PHE HIS GLN MET SEQRES 18 B 316 LEU ALA SER GLY PHE GLU ALA GLU VAL ARG ALA LEU PHE SEQRES 19 B 316 ALA ARG GLY ASP LEU HIS THR ASP LEU PRO SER ILE ARG SEQRES 20 B 316 CYS VAL GLY TYR ARG GLN MET TRP SER TYR LEU GLU GLY SEQRES 21 B 316 GLU ILE SER TYR ASP GLU MET VAL TYR ARG GLY VAL CYS SEQRES 22 B 316 ALA THR ARG GLN LEU ALA LYS ARG GLN ILE THR TRP LEU SEQRES 23 B 316 ARG GLY TRP GLU GLY VAL HIS TRP LEU ASP SER GLU LYS SEQRES 24 B 316 PRO GLU GLN ALA ARG ASP GLU VAL LEU GLN VAL VAL GLY SEQRES 25 B 316 ALA ILE ALA GLY SEQRES 1 C 76 G C C C G G A U A G C U C SEQRES 2 C 76 A G U C G G U A G A G C A SEQRES 3 C 76 G G G G A U U G A A A A U SEQRES 4 C 76 C C C C G U G U C C U U G SEQRES 5 C 76 G U U C G A U U C C G A G SEQRES 6 C 76 U C C G G G C A C C A SEQRES 1 D 76 G C C C G G A U A G C U C SEQRES 2 D 76 A G U C G G U A G A G C A SEQRES 3 D 76 G G G G A U U G A A A A U SEQRES 4 D 76 C C C C G U G U C C U U G SEQRES 5 D 76 G U U C G A U U C C G A G SEQRES 6 D 76 U C C G G G C A C C A HET DST A 317 14 HET MG A 318 1 HET DST B 317 14 HET MG B 318 1 HET MG C 77 1 HET MG C 78 1 HET MG C 79 1 HET MG C 80 1 HET MG C 81 1 HET MG C 82 1 HET MG C 83 1 HET MG D 77 1 HETNAM DST DIMETHYLALLYL S-THIOLODIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN DST DMASPP; DMAPP; DMADP; DIMETHYLALLYL PYROPHOSPHATE; HETSYN 2 DST DIMETHYLALLYL DIPHOSPHATE; ISOPRENYL PYROPHOSPHATE FORMUL 5 DST 2(C5 H12 O6 P2 S) FORMUL 6 MG 10(MG 2+) FORMUL 17 HOH *197(H2 O) HELIX 1 1 GLY A 22 LEU A 34 1 13 HELIX 2 2 ASN A 58 ALA A 65 1 8 HELIX 3 3 SER A 80 ALA A 98 1 19 HELIX 4 4 THR A 108 GLY A 118 1 11 HELIX 5 5 ASP A 126 ASP A 153 1 28 HELIX 6 6 ASP A 153 ILE A 160 1 8 HELIX 7 7 ASP A 164 GLY A 179 1 16 HELIX 8 8 THR A 181 THR A 186 1 6 HELIX 9 9 SER A 206 ALA A 223 1 18 HELIX 10 10 GLY A 225 ARG A 236 1 12 HELIX 11 11 GLY A 250 GLU A 259 1 10 HELIX 12 12 SER A 263 ARG A 287 1 25 HELIX 13 13 ALA A 303 VAL A 311 1 9 HELIX 14 14 GLY B 22 LEU B 34 1 13 HELIX 15 15 ASN B 58 ALA B 65 1 8 HELIX 16 16 SER B 80 ALA B 97 1 18 HELIX 17 17 THR B 108 GLY B 118 1 11 HELIX 18 18 GLU B 128 GLU B 139 1 12 HELIX 19 19 HIS B 146 GLN B 150 5 5 HELIX 20 20 VAL B 155 ILE B 160 1 6 HELIX 21 21 ASP B 164 GLY B 179 1 16 HELIX 22 22 THR B 181 THR B 186 1 6 HELIX 23 23 SER B 206 ALA B 223 1 18 HELIX 24 24 GLY B 225 ARG B 236 1 12 HELIX 25 25 GLY B 250 GLU B 259 1 10 HELIX 26 26 SER B 263 ARG B 287 1 25 HELIX 27 27 LYS B 299 GLN B 309 1 11 SHEET 1 A 6 HIS A 67 ARG A 68 0 SHEET 2 A 6 VAL A 36 VAL A 41 1 N SER A 40 O ARG A 68 SHEET 3 A 6 ILE A 101 GLY A 106 1 O VAL A 105 N VAL A 41 SHEET 4 A 6 LYS A 11 MET A 16 1 N LEU A 15 O LEU A 104 SHEET 5 A 6 GLN A 196 ALA A 203 1 O PHE A 200 N PHE A 14 SHEET 6 A 6 VAL A 292 ASP A 296 1 O LEU A 295 N ALA A 201 SHEET 1 B 6 HIS B 67 ARG B 68 0 SHEET 2 B 6 VAL B 36 VAL B 41 1 N SER B 40 O ARG B 68 SHEET 3 B 6 ILE B 101 GLY B 106 1 O VAL B 105 N VAL B 41 SHEET 4 B 6 LYS B 11 MET B 16 1 N LEU B 15 O LEU B 104 SHEET 5 B 6 GLN B 196 ALA B 203 1 O PHE B 200 N PHE B 14 SHEET 6 B 6 VAL B 292 ASP B 296 1 O HIS B 293 N GLN B 199 LINK OG1 THR A 24 MG MG A 318 1555 1555 2.09 LINK O5 DST A 317 MG MG A 318 1555 1555 2.29 LINK O7 DST A 317 MG MG A 318 1555 1555 2.10 LINK OG1 THR B 24 MG MG B 318 1555 1555 2.09 LINK O5 DST B 317 MG MG B 318 1555 1555 2.03 LINK O7 DST B 317 MG MG B 318 1555 1555 2.01 LINK OP1 A C 7 MG MG C 79 1555 1555 2.11 LINK O4 U C 8 MG MG C 79 1555 1555 2.25 LINK OP2 U C 12 MG MG C 83 1555 1555 2.21 LINK OP1 C C 17 MG MG C 77 1555 1555 2.45 LINK OP1 G C 19 MG MG C 77 1555 1555 2.10 LINK OP2 G C 22 MG MG C 82 1555 1555 2.22 LINK O6 G C 46 MG MG C 82 1555 1555 2.27 LINK OP2 U C 59 MG MG C 81 1555 1555 2.15 LINK OP1 U C 60 MG MG C 80 1555 1555 2.11 LINK MG MG C 79 O HOH C 112 1555 1555 2.05 LINK MG MG C 82 O HOH C 195 1555 1555 2.45 LINK N7 G D 27 MG MG D 77 1555 1555 2.28 LINK O6 G D 27 MG MG D 77 1555 1555 2.22 SITE 1 AC1 15 THR A 19 ALA A 20 SER A 21 GLY A 22 SITE 2 AC1 15 LYS A 23 THR A 24 GLY A 53 THR A 54 SITE 3 AC1 15 ARG A 217 LEU A 278 MG A 318 HOH A 343 SITE 4 AC1 15 HOH A 366 HOH A 372 A C 37 SITE 1 AC2 13 THR B 19 ALA B 20 SER B 21 GLY B 22 SITE 2 AC2 13 LYS B 23 THR B 24 THR B 54 ALA B 55 SITE 3 AC2 13 ARG B 217 MG B 318 HOH B 322 HOH B 325 SITE 4 AC2 13 HOH B 348 SITE 1 AC3 3 U C 16 C C 17 G C 19 SITE 1 AC4 2 G C 27 HOH C 108 SITE 1 AC5 5 A C 7 U C 8 A C 14 HOH C 112 SITE 2 AC5 5 HOH C 113 SITE 1 AC6 2 G D 27 HOH D 142 SITE 1 AC7 2 U C 59 U C 60 SITE 1 AC8 2 A C 58 U C 59 SITE 1 AC9 4 G C 22 U C 45 G C 46 HOH C 195 SITE 1 BC1 1 U C 12 SITE 1 BC2 2 THR A 24 DST A 317 SITE 1 BC3 3 THR B 24 ALA B 55 DST B 317 CRYST1 88.300 90.000 150.500 90.00 90.00 90.00 P 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 0.011325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011111 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006645 0.00000