HEADER LIGASE/RNA 06-APR-99 1QF6 TITLE STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE COMPLEXED WITH ITS TITLE 2 COGNATE TRNA CAVEAT 1QF6 INCORRECT CHIRAL CENTER(S) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREONINE TRNA; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: TRNA (THR); COMPND 5 OTHER_DETAILS: COMPLEXED WITH ADENOSINE MONOPHOSPHATE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THREONYL-TRNA SYNTHETASE; COMPND 8 CHAIN: A; COMPND 9 SYNONYM: THRRS; COMPND 10 EC: 6.1.1.3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 6 ORGANISM_TAXID: 562 KEYWDS THREONYL-TRNA SYNTHETASE, TRNA(THR), AMP, MRNA, AMINOACYLATION, KEYWDS 2 TRANSLATIONAL REGULATION, PROTEIN/RNA, LIGASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.SANKARANARAYANAN,A.C.DOCK-BREGEON,B.REES,D.MORAS REVDAT 8 27-DEC-23 1QF6 1 REMARK LINK REVDAT 7 13-JUL-11 1QF6 1 SHEET REVDAT 6 24-FEB-09 1QF6 1 VERSN REVDAT 5 30-MAR-04 1QF6 1 HELIX MODRES REMARK REVDAT 4 01-APR-03 1QF6 1 JRNL REVDAT 3 19-JUN-00 1QF6 1 SEQRES MODRES HETNAM HET REVDAT 3 2 1 HETATM REMARK REVDAT 2 14-JUN-00 1QF6 1 COMPND HEADER CAVEAT REVDAT 1 06-MAY-99 1QF6 0 JRNL AUTH R.SANKARANARAYANAN,A.C.DOCK-BREGEON,P.ROMBY,J.CAILLET, JRNL AUTH 2 M.SPRINGER,B.REES,C.EHRESMANN,B.EHRESMANN,D.MORAS JRNL TITL THE STRUCTURE OF THREONYL-TRNA SYNTHETASE-TRNA(THR) COMPLEX JRNL TITL 2 ENLIGHTENS ITS REPRESSOR ACTIVITY AND REVEALS AN ESSENTIAL JRNL TITL 3 ZINC ION IN THE ACTIVE SITE JRNL REF CELL(CAMBRIDGE,MASS.) V. 97 371 1999 JRNL REFN ISSN 0092-8674 JRNL PMID 10319817 JRNL DOI 10.1016/S0092-8674(00)80746-1 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 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) (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 41055 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) : 0.195 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 3118 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5862 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 463 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5192 REMARK 3 NUCLEIC ACID ATOMS : 1633 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 1.44000 REMARK 3 B12 (A**2) : 13.00000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.42 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.53 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.610 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) : 1.530 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.570 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.240 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.600 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.29 REMARK 3 BSOL : 33.76 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_C.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : AMD_NEW.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_D.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : LIGAND_NEW4.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000795. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43094 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, PEG 4000, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.85667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.71333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.71333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.85667 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: 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 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 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 O ALA A 538 NH1 ARG A 568 2.12 REMARK 500 O THR A 422 O GLU A 458 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 -0.082 REMARK 500 GLU A 146 CG GLU A 146 CD 0.126 REMARK 500 GLU A 146 CD GLU A 146 OE1 0.072 REMARK 500 GLU A 146 CD GLU A 146 OE2 0.089 REMARK 500 GLU A 391 CG GLU A 391 CD 0.097 REMARK 500 GLU A 391 CD GLU A 391 OE1 0.081 REMARK 500 GLU A 391 CD GLU A 391 OE2 0.066 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 A B 7 C2' - C3' - O3' ANGL. DEV. = 17.9 DEGREES REMARK 500 C B 48 C2' - C3' - O3' ANGL. DEV. = 16.4 DEGREES REMARK 500 PRO A 331 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 26 -27.39 -37.95 REMARK 500 ALA A 47 -6.47 -55.20 REMARK 500 ASP A 54 158.29 -43.87 REMARK 500 ALA A 93 -110.12 -109.32 REMARK 500 THR A 111 109.88 -59.30 REMARK 500 TRP A 141 -7.06 -56.93 REMARK 500 ALA A 165 105.60 -45.50 REMARK 500 HIS A 166 -14.70 -44.42 REMARK 500 ASP A 167 48.69 -109.08 REMARK 500 LYS A 169 60.07 -108.04 REMARK 500 GLU A 176 -119.36 55.36 REMARK 500 MET A 181 44.26 -154.84 REMARK 500 ARG A 183 -173.65 -37.42 REMARK 500 CYS A 193 45.74 -104.21 REMARK 500 MET A 199 -107.64 -112.07 REMARK 500 LYS A 246 -74.28 -74.47 REMARK 500 ALA A 260 58.57 -145.01 REMARK 500 GLN A 289 75.03 51.74 REMARK 500 ARG A 423 128.83 -39.21 REMARK 500 ALA A 460 153.19 -49.11 REMARK 500 ASP A 472 -169.91 -104.14 REMARK 500 CYS A 480 -96.57 -123.23 REMARK 500 SER A 494 71.07 44.33 REMARK 500 ASP A 501 10.63 -66.58 REMARK 500 THR A 535 -44.92 -26.10 REMARK 500 SER A 550 -71.65 -37.00 REMARK 500 VAL A 601 -104.55 -26.65 REMARK 500 SER A 603 -5.79 -156.55 REMARK 500 LYS A 605 -177.63 -53.52 REMARK 500 LYS A 614 91.59 169.62 REMARK 500 ASN A 622 -17.81 -49.28 REMARK 500 ARG A 633 -32.50 -38.84 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 1 0.06 SIDE CHAIN REMARK 500 G B 19 0.10 SIDE CHAIN REMARK 500 A B 21 0.08 SIDE CHAIN REMARK 500 C B 25 0.07 SIDE CHAIN REMARK 500 G B 27 0.06 SIDE CHAIN REMARK 500 A B 58 0.06 SIDE CHAIN REMARK 500 U B 63 0.07 SIDE CHAIN REMARK 500 U B 65 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 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 334 SG REMARK 620 2 HIS A 385 NE2 89.7 REMARK 620 3 HIS A 511 ND1 90.9 94.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 1002 DBREF 1QF6 A 1 642 UNP P0A8M3 SYT_ECOLI 1 642 DBREF 1QF6 B 1 76 PDB 1QF6 1QF6 1 76 SEQRES 1 B 76 G C C G A U A U A G C U C SEQRES 2 B 76 A G H2U H2U G G H2U A G A G C A SEQRES 3 B 76 G C G C A U U C G U AET A U SEQRES 4 B 76 G C G A A G G7M U C G U A G SEQRES 5 B 76 G 5MU PSU C G A C U C C U A U SEQRES 6 B 76 U A U C G G C A C C A SEQRES 1 A 642 MET PRO VAL ILE THR LEU PRO ASP GLY SER GLN ARG HIS SEQRES 2 A 642 TYR ASP HIS ALA VAL SER PRO MET ASP VAL ALA LEU ASP SEQRES 3 A 642 ILE GLY PRO GLY LEU ALA LYS ALA CYS ILE ALA GLY ARG SEQRES 4 A 642 VAL ASN GLY GLU LEU VAL ASP ALA CYS ASP LEU ILE GLU SEQRES 5 A 642 ASN ASP ALA GLN LEU SER ILE ILE THR ALA LYS ASP GLU SEQRES 6 A 642 GLU GLY LEU GLU ILE ILE ARG HIS SER CYS ALA HIS LEU SEQRES 7 A 642 LEU GLY HIS ALA ILE LYS GLN LEU TRP PRO HIS THR LYS SEQRES 8 A 642 MET ALA ILE GLY PRO VAL ILE ASP ASN GLY PHE TYR TYR SEQRES 9 A 642 ASP VAL ASP LEU ASP ARG THR LEU THR GLN GLU ASP VAL SEQRES 10 A 642 GLU ALA LEU GLU LYS ARG MET HIS GLU LEU ALA GLU LYS SEQRES 11 A 642 ASN TYR ASP VAL ILE LYS LYS LYS VAL SER TRP HIS GLU SEQRES 12 A 642 ALA ARG GLU THR PHE ALA ASN ARG GLY GLU SER TYR LYS SEQRES 13 A 642 VAL SER ILE LEU ASP GLU ASN ILE ALA HIS ASP ASP LYS SEQRES 14 A 642 PRO GLY LEU TYR PHE HIS GLU GLU TYR VAL ASP MET CYS SEQRES 15 A 642 ARG GLY PRO HIS VAL PRO ASN MET ARG PHE CYS HIS HIS SEQRES 16 A 642 PHE LYS LEU MET LYS THR ALA GLY ALA TYR TRP ARG GLY SEQRES 17 A 642 ASP SER ASN ASN LYS MET LEU GLN ARG ILE TYR GLY THR SEQRES 18 A 642 ALA TRP ALA ASP LYS LYS ALA LEU ASN ALA TYR LEU GLN SEQRES 19 A 642 ARG LEU GLU GLU ALA ALA LYS ARG ASP HIS ARG LYS ILE SEQRES 20 A 642 GLY LYS GLN LEU ASP LEU TYR HIS MET GLN GLU GLU ALA SEQRES 21 A 642 PRO GLY MET VAL PHE TRP HIS ASN ASP GLY TRP THR ILE SEQRES 22 A 642 PHE ARG GLU LEU GLU VAL PHE VAL ARG SER LYS LEU LYS SEQRES 23 A 642 GLU TYR GLN TYR GLN GLU VAL LYS GLY PRO PHE MET MET SEQRES 24 A 642 ASP ARG VAL LEU TRP GLU LYS THR GLY HIS TRP ASP ASN SEQRES 25 A 642 TYR LYS ASP ALA MET PHE THR THR SER SER GLU ASN ARG SEQRES 26 A 642 GLU TYR CYS ILE LYS PRO MET ASN CYS PRO GLY HIS VAL SEQRES 27 A 642 GLN ILE PHE ASN GLN GLY LEU LYS SER TYR ARG ASP LEU SEQRES 28 A 642 PRO LEU ARG MET ALA GLU PHE GLY SER CYS HIS ARG ASN SEQRES 29 A 642 GLU PRO SER GLY SER LEU HIS GLY LEU MET ARG VAL ARG SEQRES 30 A 642 GLY PHE THR GLN ASP ASP ALA HIS ILE PHE CYS THR GLU SEQRES 31 A 642 GLU GLN ILE ARG ASP GLU VAL ASN GLY CYS ILE ARG LEU SEQRES 32 A 642 VAL TYR ASP MET TYR SER THR PHE GLY PHE GLU LYS ILE SEQRES 33 A 642 VAL VAL LYS LEU SER THR ARG PRO GLU LYS ARG ILE GLY SEQRES 34 A 642 SER ASP GLU MET TRP ASP ARG ALA GLU ALA ASP LEU ALA SEQRES 35 A 642 VAL ALA LEU GLU GLU ASN ASN ILE PRO PHE GLU TYR GLN SEQRES 36 A 642 LEU GLY GLU GLY ALA PHE TYR GLY PRO LYS ILE GLU PHE SEQRES 37 A 642 THR LEU TYR ASP CYS LEU ASP ARG ALA TRP GLN CYS GLY SEQRES 38 A 642 THR VAL GLN LEU ASP PHE SER LEU PRO SER ARG LEU SER SEQRES 39 A 642 ALA SER TYR VAL GLY GLU ASP ASN GLU ARG LYS VAL PRO SEQRES 40 A 642 VAL MET ILE HIS ARG ALA ILE LEU GLY SER MET GLU ARG SEQRES 41 A 642 PHE ILE GLY ILE LEU THR GLU GLU PHE ALA GLY PHE PHE SEQRES 42 A 642 PRO THR TRP LEU ALA PRO VAL GLN VAL VAL ILE MET ASN SEQRES 43 A 642 ILE THR ASP SER GLN SER GLU TYR VAL ASN GLU LEU THR SEQRES 44 A 642 GLN LYS LEU SER ASN ALA GLY ILE ARG VAL LYS ALA ASP SEQRES 45 A 642 LEU ARG ASN GLU LYS ILE GLY PHE LYS ILE ARG GLU HIS SEQRES 46 A 642 THR LEU ARG ARG VAL PRO TYR MET LEU VAL CYS GLY ASP SEQRES 47 A 642 LYS GLU VAL GLU SER GLY LYS VAL ALA VAL ARG THR ARG SEQRES 48 A 642 ARG GLY LYS ASP LEU GLY SER MET ASP VAL ASN GLU VAL SEQRES 49 A 642 ILE GLU LYS LEU GLN GLN GLU ILE ARG SER ARG SER LEU SEQRES 50 A 642 LYS GLN LEU GLU GLU MODRES 1QF6 H2U B 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1QF6 H2U B 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1QF6 H2U B 20 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1QF6 AET B 37 A MODRES 1QF6 G7M B 46 G N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE MODRES 1QF6 5MU B 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1QF6 PSU B 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET H2U B 16 20 HET H2U B 17 20 HET H2U B 20 20 HET AET B 37 33 HET G7M B 46 24 HET 5MU B 54 21 HET PSU B 55 20 HET ZN A1001 1 HET AMP A1002 23 HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM AET N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL) HETNAM 2 AET METHYLCARBAMOYL]THREONINE-5'-MONOPHOSPHATE HETNAM G7M N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN AET N-(NEBULARIN-6-YL-METHYLCARBAMOYL)-L-THREONINE-5'- HETSYN 2 AET MONOPHOSPHATE FORMUL 1 H2U 3(C9 H15 N2 O9 P) FORMUL 1 AET C16 H23 N6 O11 P FORMUL 1 G7M C11 H17 N5 O8 P 1+ FORMUL 1 5MU C10 H15 N2 O9 P FORMUL 1 PSU C9 H13 N2 O9 P FORMUL 3 ZN ZN 2+ FORMUL 4 AMP C10 H14 N5 O7 P FORMUL 5 HOH *244(H2 O) HELIX 1 1 SER A 19 GLY A 28 1 10 HELIX 2 2 GLY A 28 CYS A 35 1 8 HELIX 3 3 ASP A 64 TRP A 87 1 24 HELIX 4 4 THR A 113 LYS A 130 1 18 HELIX 5 5 SER A 140 GLY A 152 1 13 HELIX 6 6 GLU A 153 ILE A 164 1 12 HELIX 7 7 ASN A 189 CYS A 193 5 5 HELIX 8 8 ARG A 207 ASP A 209 5 3 HELIX 9 9 ASP A 225 LYS A 241 1 17 HELIX 10 10 ASP A 243 LEU A 251 1 9 HELIX 11 11 HIS A 267 TYR A 288 1 22 HELIX 12 12 ARG A 301 GLY A 308 1 8 HELIX 13 13 GLY A 308 LYS A 314 1 7 HELIX 14 14 ASP A 315 MET A 317 5 3 HELIX 15 15 ASN A 333 ASN A 342 1 10 HELIX 16 16 ARG A 349 LEU A 351 5 3 HELIX 17 17 PRO A 366 LEU A 370 5 5 HELIX 18 18 THR A 389 GLU A 391 5 3 HELIX 19 19 GLN A 392 SER A 409 1 18 HELIX 20 20 THR A 410 GLY A 412 5 3 HELIX 21 21 SER A 430 GLU A 447 1 18 HELIX 22 22 SER A 488 LEU A 493 1 6 HELIX 23 23 MET A 518 ALA A 530 1 13 HELIX 24 24 THR A 548 ASN A 564 1 17 HELIX 25 25 LYS A 577 ARG A 588 1 12 HELIX 26 26 GLU A 600 GLY A 604 5 5 HELIX 27 27 ASP A 620 SER A 634 1 15 SHEET 1 A 3 GLN A 11 HIS A 13 0 SHEET 2 A 3 VAL A 3 THR A 5 -1 N ILE A 4 O ARG A 12 SHEET 3 A 3 ALA A 55 GLN A 56 1 O ALA A 55 N THR A 5 SHEET 1 B 3 GLU A 43 ASP A 46 0 SHEET 2 B 3 ALA A 37 VAL A 40 -1 N GLY A 38 O VAL A 45 SHEET 3 B 3 ILE A 59 ILE A 60 -1 O ILE A 60 N ALA A 37 SHEET 1 C 3 LYS A 91 MET A 92 0 SHEET 2 C 3 GLY A 101 ASP A 107 -1 O ASP A 107 N LYS A 91 SHEET 3 C 3 VAL A 97 ILE A 98 -1 N ILE A 98 O GLY A 101 SHEET 1 D 4 LYS A 91 MET A 92 0 SHEET 2 D 4 GLY A 101 ASP A 107 -1 O ASP A 107 N LYS A 91 SHEET 3 D 4 MET A 214 ALA A 222 -1 O GLY A 220 N PHE A 102 SHEET 4 D 4 PHE A 196 TYR A 205 -1 N ALA A 202 O ARG A 217 SHEET 1 E 3 VAL A 134 LYS A 138 0 SHEET 2 E 3 GLY A 171 HIS A 175 -1 O PHE A 174 N ILE A 135 SHEET 3 E 3 TYR A 178 ASP A 180 -1 O ASP A 180 N TYR A 173 SHEET 1 F 2 TYR A 254 HIS A 255 0 SHEET 2 F 2 PHE A 265 TRP A 266 -1 O PHE A 265 N HIS A 255 SHEET 1 G 8 GLN A 291 GLU A 292 0 SHEET 2 G 8 LEU A 353 HIS A 362 1 O ALA A 356 N GLN A 291 SHEET 3 G 8 GLY A 378 CYS A 388 -1 O PHE A 387 N LEU A 353 SHEET 4 G 8 VAL A 508 SER A 517 -1 O VAL A 508 N CYS A 388 SHEET 5 G 8 ALA A 477 ASP A 486 -1 N GLN A 484 O HIS A 511 SHEET 6 G 8 LYS A 465 TYR A 471 -1 N PHE A 468 O CYS A 480 SHEET 7 G 8 VAL A 417 SER A 421 -1 N VAL A 417 O THR A 469 SHEET 8 G 8 GLU A 453 GLN A 455 1 O GLN A 455 N LEU A 420 SHEET 1 H 3 MET A 298 ASP A 300 0 SHEET 2 H 3 ARG A 325 ILE A 329 -1 O CYS A 328 N MET A 299 SHEET 3 H 3 PHE A 318 SER A 322 -1 N SER A 322 O ARG A 325 SHEET 1 I 3 LYS A 346 SER A 347 0 SHEET 2 I 3 TYR A 497 VAL A 498 1 O VAL A 498 N LYS A 346 SHEET 3 I 3 ARG A 504 LYS A 505 -1 O LYS A 505 N TYR A 497 SHEET 1 J 5 VAL A 569 ASP A 572 0 SHEET 2 J 5 VAL A 542 ASN A 546 1 N VAL A 542 O LYS A 570 SHEET 3 J 5 TYR A 592 CYS A 596 1 O LEU A 594 N MET A 545 SHEET 4 J 5 VAL A 606 THR A 610 -1 O ARG A 609 N MET A 593 SHEET 5 J 5 ASP A 615 MET A 619 -1 O LEU A 616 N VAL A 608 LINK O3' G B 15 P H2U B 16 1555 1555 1.61 LINK O3' H2U B 16 P H2U B 17 1555 1555 1.62 LINK O3' H2U B 17 P G B 18 1555 1555 1.60 LINK O3' G B 19 P H2U B 20 1555 1555 1.61 LINK O3' H2U B 20 P A B 21 1555 1555 1.61 LINK O3' U B 36 P AET B 37 1555 1555 1.60 LINK O3' AET B 37 P A B 38 1555 1555 1.60 LINK O3' G B 45 P G7M B 46 1555 1555 1.61 LINK O3' G7M B 46 P U B 47 1555 1555 1.58 LINK O3' G B 53 P 5MU B 54 1555 1555 1.61 LINK O3' 5MU B 54 P PSU B 55 1555 1555 1.61 LINK O3' PSU B 55 P C B 56 1555 1555 1.61 LINK SG CYS A 334 ZN ZN A1001 1555 1555 2.32 LINK NE2 HIS A 385 ZN ZN A1001 1555 1555 2.18 LINK ND1 HIS A 511 ZN ZN A1001 1555 1555 2.42 CISPEP 1 LEU A 351 PRO A 352 0 0.04 SITE 1 AC1 4 CYS A 334 HIS A 385 HIS A 511 HOH A1123 SITE 1 AC2 15 ARG A 363 GLU A 365 MET A 374 ARG A 375 SITE 2 AC2 15 VAL A 376 PHE A 379 GLN A 381 GLN A 479 SITE 3 AC2 15 CYS A 480 THR A 482 GLY A 516 SER A 517 SITE 4 AC2 15 ARG A 520 HOH A1118 A B 76 CRYST1 162.670 162.670 128.570 90.00 90.00 120.00 P 31 2 1 6 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 0.006147 0.003549 0.000000 0.00000 SCALE2 0.000000 0.007098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007778 0.00000