HEADER LIGASE/RNA 01-APR-13 4JYZ TITLE CRYSTAL STRUCTURE OF E. COLI GLUTAMINYL-TRNA SYNTHETASE BOUND TO ATP TITLE 2 AND NATIVE TRNA(GLN) CONTAINING THE CMNM5S2U34 ANTICODON WOBBLE BASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTAMINYL-TRNA SYNTHETASE, GLNRS; COMPND 5 EC: 6.1.1.18; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (72-MER); COMPND 9 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GLNS, B0680, JW0666; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS ROSSMANN FOLD, PROTEIN-RNA COMPLEX, AMINOACYL-TRNA SYNTHETASE, KEYWDS 2 LIGASE, LIGASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.J.PERONA,A.RODRIGUEZ-HERNANDEZ REVDAT 4 28-FEB-24 4JYZ 1 REMARK LINK REVDAT 3 23-OCT-13 4JYZ 1 JRNL REVDAT 2 21-AUG-13 4JYZ 1 JRNL REVDAT 1 29-MAY-13 4JYZ 0 JRNL AUTH A.RODRIGUEZ-HERNANDEZ,J.L.SPEARS,K.W.GASTON,P.A.LIMBACH, JRNL AUTH 2 H.GAMPER,Y.M.HOU,R.KAISER,P.F.AGRIS,J.J.PERONA JRNL TITL STRUCTURAL AND MECHANISTIC BASIS FOR ENHANCED TRANSLATIONAL JRNL TITL 2 EFFICIENCY BY 2-THIOURIDINE AT THE TRNA ANTICODON WOBBLE JRNL TITL 3 POSITION. JRNL REF J.MOL.BIOL. V. 425 3888 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23727144 JRNL DOI 10.1016/J.JMB.2013.05.018 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.60 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 43186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4103 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4328 REMARK 3 NUCLEIC ACID ATOMS : 1543 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.52 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) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.389 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000078681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 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 : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44106 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.740 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS 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 (%): 65.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.36-0.4 W/V SODIUM CITRATE, 40 MM REMARK 280 PIPES, 20 MM MGSO4, 20 MM B-MERCAPTOETHANOL, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 56.85000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.85000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.70000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 117.31000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.70000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 117.31000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.85000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.70000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 117.31000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.85000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.70000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 117.31000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 772 LIES ON A SPECIAL POSITION. 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 SER A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 4 REMARK 465 ALA A 5 REMARK 465 ARG A 6 REMARK 465 ALA A 549 REMARK 465 LYS A 550 REMARK 465 VAL A 551 REMARK 465 GLY A 552 REMARK 465 GLU A 553 REMARK 465 U B 901 REMARK 465 U B 946 REMARK 465 U B 947 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 GLN A 357 CG CD OE1 NE2 REMARK 470 GLU A 395 CG CD OE1 OE2 REMARK 470 LYS A 398 CG CD CE NZ REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 VAL A 404 CG1 CG2 REMARK 470 LEU A 405 CG CD1 CD2 REMARK 470 LYS A 407 CG CD CE NZ REMARK 470 GLU A 423 CG CD OE1 OE2 REMARK 470 ASP A 440 CG OD1 OD2 REMARK 470 SER A 443 OG REMARK 470 LYS A 444 CG CD CE NZ REMARK 470 ASP A 445 CG OD1 OD2 REMARK 470 ASP A 448 CG OD1 OD2 REMARK 470 LYS A 453 CG CD CE NZ REMARK 470 HIS A 463 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 527 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 PRO A 369 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 U B 960 C2' - C3' - O3' ANGL. DEV. = 10.9 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 PRO A 32 75.69 -114.14 REMARK 500 ILE A 176 -103.87 -120.14 REMARK 500 THR A 316 -159.43 -140.21 REMARK 500 GLU A 361 -165.66 -164.82 REMARK 500 HIS A 368 98.22 -173.20 REMARK 500 PRO A 369 -26.80 -36.68 REMARK 500 SER A 382 -163.74 -101.53 REMARK 500 ARG A 402 -134.25 -75.70 REMARK 500 ALA A 414 -150.77 -155.83 REMARK 500 GLU A 420 -57.88 -132.32 REMARK 500 ASP A 440 51.66 -99.18 REMARK 500 THR A 441 -73.40 -114.86 REMARK 500 LEU A 442 -99.60 24.24 REMARK 500 LYS A 444 -172.14 176.09 REMARK 500 ASP A 445 129.65 59.91 REMARK 500 PRO A 446 38.59 -88.80 REMARK 500 ALA A 447 -97.19 62.97 REMARK 500 ARG A 450 104.84 -59.68 REMARK 500 ALA A 462 -75.14 -57.35 REMARK 500 ALA A 464 102.11 32.77 REMARK 500 PRO A 466 87.17 -66.14 REMARK 500 ASN A 480 68.74 -119.76 REMARK 500 LEU A 507 2.51 -68.02 REMARK 500 GLU A 521 -63.26 -125.78 REMARK 500 ARG A 545 107.34 -57.38 REMARK 500 THR A 547 109.39 169.70 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 919 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE CHIRALITY FOR THE DEFINED NUCLEOTIDE-BASE 1RN IS BASED ON THE REMARK 600 MODELED COORDINATES REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JXZ RELATED DB: PDB REMARK 900 THE SAME STRUCTURE WITH AN UNMODIFIED TRNA(GLN) TRANSCRIPT REMARK 900 CONTAINING THE UUG ANTICODON REMARK 900 RELATED ID: 4JXX RELATED DB: PDB DBREF 4JYZ A 1 553 UNP P00962 SYQ_ECOLI 2 554 DBREF 4JYZ B 901 976 PDB 4JYZ 4JYZ 901 976 SEQRES 1 A 553 SER GLU ALA GLU ALA ARG PRO THR ASN PHE ILE ARG GLN SEQRES 2 A 553 ILE ILE ASP GLU ASP LEU ALA SER GLY LYS HIS THR THR SEQRES 3 A 553 VAL HIS THR ARG PHE PRO PRO GLU PRO ASN GLY TYR LEU SEQRES 4 A 553 HIS ILE GLY HIS ALA LYS SER ILE CYS LEU ASN PHE GLY SEQRES 5 A 553 ILE ALA GLN ASP TYR LYS GLY GLN CYS ASN LEU ARG PHE SEQRES 6 A 553 ASP ASP THR ASN PRO VAL LYS GLU ASP ILE GLU TYR VAL SEQRES 7 A 553 GLU SER ILE LYS ASN ASP VAL GLU TRP LEU GLY PHE HIS SEQRES 8 A 553 TRP SER GLY ASN VAL ARG TYR SER SER ASP TYR PHE ASP SEQRES 9 A 553 GLN LEU HIS ALA TYR ALA ILE GLU LEU ILE ASN LYS GLY SEQRES 10 A 553 LEU ALA TYR VAL ASP GLU LEU THR PRO GLU GLN ILE ARG SEQRES 11 A 553 GLU TYR ARG GLY THR LEU THR GLN PRO GLY LYS ASN SER SEQRES 12 A 553 PRO TYR ARG ASP ARG SER VAL GLU GLU ASN LEU ALA LEU SEQRES 13 A 553 PHE GLU LYS MET ARG ALA GLY GLY PHE GLU GLU GLY LYS SEQRES 14 A 553 ALA CYS LEU ARG ALA LYS ILE ASP MET ALA SER PRO PHE SEQRES 15 A 553 ILE VAL MET ARG ASP PRO VAL LEU TYR ARG ILE LYS PHE SEQRES 16 A 553 ALA GLU HIS HIS GLN THR GLY ASN LYS TRP CYS ILE TYR SEQRES 17 A 553 PRO MET TYR ASP PHE THR HIS CYS ILE SER ASP ALA LEU SEQRES 18 A 553 GLU GLY ILE THR HIS SER LEU CYS THR LEU GLU PHE GLN SEQRES 19 A 553 ASP ASN ARG ARG LEU TYR ASP TRP VAL LEU ASP ASN ILE SEQRES 20 A 553 THR ILE PRO VAL HIS PRO ARG GLN TYR GLU PHE SER ARG SEQRES 21 A 553 LEU ASN LEU GLU TYR THR VAL MET SER LYS ARG LYS LEU SEQRES 22 A 553 ASN LEU LEU VAL THR ASP LYS HIS VAL GLU GLY TRP ASP SEQRES 23 A 553 ASP PRO ARG MET PRO THR ILE SER GLY LEU ARG ARG ARG SEQRES 24 A 553 GLY TYR THR ALA ALA SER ILE ARG GLU PHE CYS LYS ARG SEQRES 25 A 553 ILE GLY VAL THR LYS GLN ASP ASN THR ILE GLU MET ALA SEQRES 26 A 553 SER LEU GLU SER CYS ILE ARG GLU ASP LEU ASN GLU ASN SEQRES 27 A 553 ALA PRO ARG ALA MET ALA VAL ILE ASP PRO VAL LYS LEU SEQRES 28 A 553 VAL ILE GLU ASN TYR GLN GLY GLU GLY GLU MET VAL THR SEQRES 29 A 553 MET PRO ASN HIS PRO ASN LYS PRO GLU MET GLY SER ARG SEQRES 30 A 553 GLN VAL PRO PHE SER GLY GLU ILE TRP ILE ASP ARG ALA SEQRES 31 A 553 ASP PHE ARG GLU GLU ALA ASN LYS GLN TYR LYS ARG LEU SEQRES 32 A 553 VAL LEU GLY LYS GLU VAL ARG LEU ARG ASN ALA TYR VAL SEQRES 33 A 553 ILE LYS ALA GLU ARG VAL GLU LYS ASP ALA GLU GLY ASN SEQRES 34 A 553 ILE THR THR ILE PHE CYS THR TYR ASP ALA ASP THR LEU SEQRES 35 A 553 SER LYS ASP PRO ALA ASP GLY ARG LYS VAL LYS GLY VAL SEQRES 36 A 553 ILE HIS TRP VAL SER ALA ALA HIS ALA LEU PRO VAL GLU SEQRES 37 A 553 ILE ARG LEU TYR ASP ARG LEU PHE SER VAL PRO ASN PRO SEQRES 38 A 553 GLY ALA ALA ASP ASP PHE LEU SER VAL ILE ASN PRO GLU SEQRES 39 A 553 SER LEU VAL ILE LYS GLN GLY PHE ALA GLU PRO SER LEU SEQRES 40 A 553 LYS ASP ALA VAL ALA GLY LYS ALA PHE GLN PHE GLU ARG SEQRES 41 A 553 GLU GLY TYR PHE CYS LEU ASP SER ARG HIS SER THR ALA SEQRES 42 A 553 GLU LYS PRO VAL PHE ASN ARG THR VAL GLY LEU ARG ASP SEQRES 43 A 553 THR TRP ALA LYS VAL GLY GLU SEQRES 1 B 75 U G G G G U A 4SU C G C C A SEQRES 2 B 75 A G C OMG G H2U A A G G C A C SEQRES 3 B 75 C G G U OMU U 1RN U G 2MA PSU A C SEQRES 4 B 75 C G G C A U U C G C A G G SEQRES 5 B 75 5MU PSU C G A A U C C U G C U SEQRES 6 B 75 A C C C C A G C C A MODRES 4JYZ 4SU B 908 U 4-THIOURIDINE-5'-MONOPHOSPHATE MODRES 4JYZ OMG B 918 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 4JYZ H2U B 920 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 4JYZ OMU B 932 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 4JYZ 1RN B 934 U MODRES 4JYZ 2MA B 937 A 2-METHYLADENOSINE-5'-MONOPHOSPHATE MODRES 4JYZ PSU B 938 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 4JYZ 5MU B 954 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 4JYZ PSU B 955 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET 4SU B 908 20 HET OMG B 918 24 HET H2U B 920 20 HET OMU B 932 21 HET 1RN B 934 26 HET 2MA B 937 23 HET PSU B 938 20 HET 5MU B 954 21 HET PSU B 955 20 HET ATP A 601 31 HET SO4 A 602 5 HET SO4 A 603 5 HETNAM 4SU 4-THIOURIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM 1RN (E)-N-{[4-OXO-1-(5-O-PHOSPHONO-BETA-D- HETNAM 2 1RN ARABINOFURANOSYL)-2-THIOXO-1,2,3,4- HETNAM 3 1RN TETRAHYDROPYRIMIDIN-5-YL]METHYLIDENE}GLYCINE HETNAM 2MA 2-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 4SU C9 H13 N2 O8 P S FORMUL 2 OMG C11 H16 N5 O8 P FORMUL 2 H2U C9 H15 N2 O9 P FORMUL 2 OMU C10 H15 N2 O9 P FORMUL 2 1RN C12 H16 N3 O10 P S FORMUL 2 2MA C11 H16 N5 O7 P FORMUL 2 PSU 2(C9 H13 N2 O9 P) FORMUL 2 5MU C10 H15 N2 O9 P FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *110(H2 O) HELIX 1 1 ASN A 9 SER A 21 1 13 HELIX 2 2 HIS A 40 TYR A 57 1 18 HELIX 3 3 ASN A 69 GLU A 73 5 5 HELIX 4 4 ASP A 74 LEU A 88 1 15 HELIX 5 5 TYR A 102 LYS A 116 1 15 HELIX 6 6 THR A 125 GLY A 134 1 10 HELIX 7 7 SER A 149 GLY A 163 1 15 HELIX 8 8 PHE A 182 ARG A 186 5 5 HELIX 9 9 MET A 210 GLY A 223 1 14 HELIX 10 10 PHE A 233 ILE A 247 1 15 HELIX 11 11 SER A 269 ASP A 279 1 11 HELIX 12 12 THR A 292 GLY A 300 1 9 HELIX 13 13 THR A 302 GLY A 314 1 13 HELIX 14 14 GLU A 323 GLU A 337 1 15 HELIX 15 15 LYS A 371 MET A 374 5 4 HELIX 16 16 ASN A 480 ALA A 484 5 5 HELIX 17 17 ASP A 486 ILE A 491 5 6 HELIX 18 18 PRO A 505 ALA A 510 5 6 SHEET 1 A 3 HIS A 28 PHE A 31 0 SHEET 2 A 3 GLN A 60 PHE A 65 1 O ASN A 62 N PHE A 31 SHEET 3 A 3 ARG A 97 TYR A 98 1 O ARG A 97 N LEU A 63 SHEET 1 B 4 ALA A 119 ASP A 122 0 SHEET 2 B 4 CYS A 171 ALA A 174 -1 O ARG A 173 N TYR A 120 SHEET 3 B 4 VAL A 189 ILE A 193 -1 O LEU A 190 N LEU A 172 SHEET 4 B 4 ILE A 207 PRO A 209 -1 O TYR A 208 N ARG A 192 SHEET 1 C 2 HIS A 226 THR A 230 0 SHEET 2 C 2 ARG A 254 PHE A 258 1 O ARG A 254 N SER A 227 SHEET 1 D 7 ARG A 341 ALA A 342 0 SHEET 2 D 7 PHE A 516 PHE A 518 1 O GLN A 517 N ALA A 342 SHEET 3 D 7 GLY A 522 LEU A 526 -1 O PHE A 524 N PHE A 516 SHEET 4 D 7 VAL A 537 GLY A 543 -1 O ASN A 539 N CYS A 525 SHEET 5 D 7 LEU A 465 TYR A 472 1 N ARG A 470 O PHE A 538 SHEET 6 D 7 LEU A 496 ALA A 503 -1 O LYS A 499 N ILE A 469 SHEET 7 D 7 ALA A 344 VAL A 345 -1 N VAL A 345 O PHE A 502 SHEET 1 E 2 PRO A 348 LYS A 350 0 SHEET 2 E 2 TRP A 386 ASP A 388 -1 O ILE A 387 N VAL A 349 SHEET 1 F 2 GLU A 361 PRO A 366 0 SHEET 2 F 2 SER A 376 PHE A 381 -1 O VAL A 379 N VAL A 363 SHEET 1 G 2 PHE A 392 ARG A 393 0 SHEET 2 G 2 LEU A 403 VAL A 404 1 O LEU A 403 N ARG A 393 SHEET 1 H 2 ARG A 410 LEU A 411 0 SHEET 2 H 2 VAL A 455 ILE A 456 1 O ILE A 456 N ARG A 410 SHEET 1 I 2 ILE A 417 LYS A 424 0 SHEET 2 I 2 ILE A 430 TYR A 437 -1 O THR A 431 N GLU A 423 LINK O3' A B 907 P 4SU B 908 1555 1555 1.60 LINK O3' 4SU B 908 P C B 909 1555 1555 1.61 LINK O3' C B 916 P OMG B 918 1555 1555 1.60 LINK O3' OMG B 918 P G B 919 1555 1555 1.61 LINK O3' G B 919 P H2U B 920 1555 1555 1.62 LINK O3' H2U B 920 P A B 921 1555 1555 1.61 LINK O3' U B 931 P OMU B 932 1555 1555 1.60 LINK O3' OMU B 932 P U B 933 1555 1555 1.61 LINK O3' U B 933 P 1RN B 934 1555 1555 1.61 LINK O3' 1RN B 934 P U B 935 1555 1555 1.60 LINK O3' G B 936 P 2MA B 937 1555 1555 1.60 LINK O3' 2MA B 937 P PSU B 938 1555 1555 1.61 LINK O3' PSU B 938 P A B 939 1555 1555 1.61 LINK O3' G B 953 P 5MU B 954 1555 1555 1.61 LINK O3' 5MU B 954 P PSU B 955 1555 1555 1.61 LINK O3' PSU B 955 P C B 956 1555 1555 1.61 SITE 1 AC1 13 PRO A 32 GLU A 34 HIS A 40 GLY A 42 SITE 2 AC1 13 HIS A 43 SER A 46 THR A 230 ARG A 260 SITE 3 AC1 13 LEU A 261 MET A 268 LYS A 270 HOH A 705 SITE 4 AC1 13 A B 976 SITE 1 AC2 6 VAL A 267 MET A 268 SER A 269 LYS A 272 SITE 2 AC2 6 GLY A 482 HOH A 771 SITE 1 AC3 3 MET A 290 LEU A 296 MET A 324 CRYST1 93.400 234.620 113.700 90.00 90.00 90.00 C 2 2 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 0.010707 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008795 0.00000