HEADER LIGASE 08-JUN-04 1TKE TITLE CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE TITLE 2 COMPLEXED WITH SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THREONYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAINS N1 AND N2 (RESIDUES 1-224); COMPND 5 SYNONYM: THREONINE--TRNA LIGASE, THRRS; COMPND 6 EC: 6.1.1.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: THRS, B1719, C2116, SF1512, S1630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.C.DOCK-BREGEON,B.REES,A.TORRES-LARIOS,G.BEY,J.CAILLET,D.MORAS REVDAT 3 23-AUG-23 1TKE 1 REMARK REVDAT 2 24-FEB-09 1TKE 1 VERSN REVDAT 1 30-NOV-04 1TKE 0 JRNL AUTH A.C.DOCK-BREGEON,B.REES,A.TORRES-LARIOS,G.BEY,J.CAILLET, JRNL AUTH 2 D.MORAS JRNL TITL ACHIEVING ERROR-FREE TRANSLATION; THE MECHANISM OF JRNL TITL 2 PROOFREADING OF THREONYL-TRNA SYNTHETASE AT ATOMIC JRNL TITL 3 RESOLUTION. JRNL REF MOL.CELL V. 16 375 2004 JRNL REFN ISSN 1097-2765 JRNL PMID 15525511 JRNL DOI 10.1016/J.MOLCEL.2004.10.002 REMARK 2 REMARK 2 RESOLUTION. 1.46 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1293636.700 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 40336 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) : 0.178 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2017 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3453 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 200 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1786 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 409 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -0.85000 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) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 4.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : 1.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.530 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.800 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 49.81 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TKE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : SI111 OR SI311 CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40336 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 24.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1QF6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS.CL, MAGNESIUM CHLORIDE, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K 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 21.84850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.30350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.45650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.30350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.84850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.45650 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 93 -102.68 -103.27 REMARK 500 ASN A 100 40.26 71.04 REMARK 500 GLU A 176 -119.91 56.01 REMARK 500 MET A 199 -110.21 -115.55 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 SER A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QF6 RELATED DB: PDB REMARK 900 THREONYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(THR) REMARK 900 RELATED ID: 1TJE RELATED DB: PDB REMARK 900 THE SAME PROTEIN DOMAINS IN THE APO FORM REMARK 900 RELATED ID: 1TKG RELATED DB: PDB REMARK 900 RELATED ID: 1TKY RELATED DB: PDB DBREF 1TKE A 1 224 UNP P0A8M3 SYT_ECOLI 1 224 SEQRES 1 A 224 MET PRO VAL ILE THR LEU PRO ASP GLY SER GLN ARG HIS SEQRES 2 A 224 TYR ASP HIS ALA VAL SER PRO MET ASP VAL ALA LEU ASP SEQRES 3 A 224 ILE GLY PRO GLY LEU ALA LYS ALA CYS ILE ALA GLY ARG SEQRES 4 A 224 VAL ASN GLY GLU LEU VAL ASP ALA CYS ASP LEU ILE GLU SEQRES 5 A 224 ASN ASP ALA GLN LEU SER ILE ILE THR ALA LYS ASP GLU SEQRES 6 A 224 GLU GLY LEU GLU ILE ILE ARG HIS SER CYS ALA HIS LEU SEQRES 7 A 224 LEU GLY HIS ALA ILE LYS GLN LEU TRP PRO HIS THR LYS SEQRES 8 A 224 MET ALA ILE GLY PRO VAL ILE ASP ASN GLY PHE TYR TYR SEQRES 9 A 224 ASP VAL ASP LEU ASP ARG THR LEU THR GLN GLU ASP VAL SEQRES 10 A 224 GLU ALA LEU GLU LYS ARG MET HIS GLU LEU ALA GLU LYS SEQRES 11 A 224 ASN TYR ASP VAL ILE LYS LYS LYS VAL SER TRP HIS GLU SEQRES 12 A 224 ALA ARG GLU THR PHE ALA ASN ARG GLY GLU SER TYR LYS SEQRES 13 A 224 VAL SER ILE LEU ASP GLU ASN ILE ALA HIS ASP ASP LYS SEQRES 14 A 224 PRO GLY LEU TYR PHE HIS GLU GLU TYR VAL ASP MET CYS SEQRES 15 A 224 ARG GLY PRO HIS VAL PRO ASN MET ARG PHE CYS HIS HIS SEQRES 16 A 224 PHE LYS LEU MET LYS THR ALA GLY ALA TYR TRP ARG GLY SEQRES 17 A 224 ASP SER ASN ASN LYS MET LEU GLN ARG ILE TYR GLY THR SEQRES 18 A 224 ALA TRP ALA HET SER A 500 7 HETNAM SER SERINE FORMUL 2 SER C3 H7 N O3 FORMUL 3 HOH *409(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 GLU A 129 1 17 HELIX 5 5 SER A 140 ARG A 151 1 12 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 SHEET 1 A 5 GLN A 11 HIS A 13 0 SHEET 2 A 5 VAL A 3 THR A 5 -1 N ILE A 4 O ARG A 12 SHEET 3 A 5 ALA A 55 ILE A 60 1 O LEU A 57 N THR A 5 SHEET 4 A 5 ALA A 37 VAL A 40 -1 N ALA A 37 O ILE A 60 SHEET 5 A 5 GLU A 43 ASP A 46 -1 O GLU A 43 N VAL A 40 SHEET 1 B 3 LYS A 91 MET A 92 0 SHEET 2 B 3 GLY A 101 ASP A 107 -1 O ASP A 107 N LYS A 91 SHEET 3 B 3 VAL A 97 ILE A 98 -1 N ILE A 98 O GLY A 101 SHEET 1 C 4 LYS A 91 MET A 92 0 SHEET 2 C 4 GLY A 101 ASP A 107 -1 O ASP A 107 N LYS A 91 SHEET 3 C 4 MET A 214 ALA A 222 -1 O GLY A 220 N PHE A 102 SHEET 4 C 4 PHE A 196 TYR A 205 -1 N ALA A 202 O ARG A 217 SHEET 1 D 3 ILE A 135 LYS A 138 0 SHEET 2 D 3 GLY A 171 HIS A 175 -1 O PHE A 174 N ILE A 135 SHEET 3 D 3 TYR A 178 CYS A 182 -1 O TYR A 178 N HIS A 175 CISPEP 1 GLY A 184 PRO A 185 0 0.13 SITE 1 AC1 11 HIS A 73 ALA A 76 HIS A 77 ILE A 94 SITE 2 AC1 11 GLY A 95 TYR A 104 ASP A 180 MET A 181 SITE 3 AC1 11 CYS A 182 HOH A 698 HOH A 887 CRYST1 43.697 44.913 116.607 90.00 90.00 90.00 P 21 21 21 4 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 0.022885 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008576 0.00000