HEADER LIGASE 11-OCT-06 2IP1 TITLE CRYSTAL STRUCTURE ANALYSIS OF S. CEREVISIAE TRYPTOPHANYL TRNA TITLE 2 SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHANYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRYPTOPHAN-TRNA LIGASE, TRPRS; COMPND 5 EC: 6.1.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: WRS1; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: BG2483 KEYWDS ROSSMANN FOLD, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, CENTER FOR HIGH-THROUGHPUT STRUCTURAL BIOLOGY, CHTSB, KEYWDS 3 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.G.MALKOWSKI,CENTER FOR HIGH-THROUGHPUT STRUCTURAL BIOLOGY (CHTSB) REVDAT 5 21-FEB-24 2IP1 1 REMARK REVDAT 4 18-OCT-17 2IP1 1 REMARK REVDAT 3 13-JUL-11 2IP1 1 VERSN REVDAT 2 24-FEB-09 2IP1 1 VERSN REVDAT 1 26-JUN-07 2IP1 0 JRNL AUTH M.G.MALKOWSKI,E.QUARTLEY,A.E.FRIEDMAN,J.BABULSKI,Y.KON, JRNL AUTH 2 J.WOLFLEY,M.SAID,J.R.LUFT,E.M.PHIZICKY,G.T.DETITTA, JRNL AUTH 3 E.J.GRAYHACK JRNL TITL BLOCKING S-ADENOSYLMETHIONINE SYNTHESIS IN YEAST ALLOWS JRNL TITL 2 SELENOMETHIONINE INCORPORATION AND MULTIWAVELENGTH ANOMALOUS JRNL TITL 3 DISPERSION PHASING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 6678 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17426150 JRNL DOI 10.1073/PNAS.0610337104 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 43259 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 + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2288 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2191 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2938 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.11000 REMARK 3 B22 (A**2) : 1.11000 REMARK 3 B33 (A**2) : -2.22000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.921 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3108 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4196 ; 1.343 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 5.654 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;33.092 ;23.919 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 503 ;13.702 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.679 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 450 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2371 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1506 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2165 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 275 ; 0.163 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 64 ; 0.165 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.205 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1910 ; 0.762 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3015 ; 1.173 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1326 ; 2.163 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1175 ; 3.369 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 99 A 153 REMARK 3 ORIGIN FOR THE GROUP (A): 10.4510 49.8880 124.4070 REMARK 3 T TENSOR REMARK 3 T11: -.0041 T22: .0435 REMARK 3 T33: -.0545 T12: .0612 REMARK 3 T13: .0461 T23: -.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.5207 L22: .7982 REMARK 3 L33: 1.8839 L12: .1595 REMARK 3 L13: .2170 L23: -.1361 REMARK 3 S TENSOR REMARK 3 S11: .0455 S12: .2269 S13: .0415 REMARK 3 S21: -.2271 S22: -.0263 S23: -.0502 REMARK 3 S31: .1466 S32: .3544 S33: -.0192 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 154 A 362 REMARK 3 RESIDUE RANGE : A 453 A 471 REMARK 3 ORIGIN FOR THE GROUP (A): -1.2300 54.6690 140.8240 REMARK 3 T TENSOR REMARK 3 T11: .0052 T22: -.0006 REMARK 3 T33: -.0216 T12: .0262 REMARK 3 T13: .0082 T23: -.0059 REMARK 3 L TENSOR REMARK 3 L11: .2245 L22: .0746 REMARK 3 L33: 1.1183 L12: .0748 REMARK 3 L13: .0040 L23: -.0892 REMARK 3 S TENSOR REMARK 3 S11: .0051 S12: .0213 S13: .0013 REMARK 3 S21: -.0265 S22: .0121 S23: -.0237 REMARK 3 S31: .0166 S32: .0083 S33: -.0173 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 363 A 452 REMARK 3 ORIGIN FOR THE GROUP (A): -5.6540 67.6630 114.1090 REMARK 3 T TENSOR REMARK 3 T11: -.0276 T22: .0290 REMARK 3 T33: -.0240 T12: -.0042 REMARK 3 T13: .0115 T23: .0029 REMARK 3 L TENSOR REMARK 3 L11: .2471 L22: 1.3065 REMARK 3 L33: 2.3654 L12: .3726 REMARK 3 L13: -.7007 L23: -1.5875 REMARK 3 S TENSOR REMARK 3 S11: -.0331 S12: .0821 S13: .0209 REMARK 3 S21: -.0613 S22: .0417 S23: -.0243 REMARK 3 S31: .0618 S32: -.0942 S33: -.0086 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2IP1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-06 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 : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935, 0.97952, 0.96109 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45655 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80% PEG 400, 100 MM NH4BR, 100MM MOPS, REMARK 280 PH 7.0, MICROBATCH UNDER OIL, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 156.82000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.17500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 235.23000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.17500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.17500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.41000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.17500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.17500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 235.23000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.17500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.17500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 78.41000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 156.82000 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 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 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 54 REMARK 465 SER A 55 REMARK 465 ASN A 56 REMARK 465 ASP A 57 REMARK 465 GLU A 58 REMARK 465 THR A 59 REMARK 465 VAL A 60 REMARK 465 GLU A 61 REMARK 465 LYS A 62 REMARK 465 VAL A 63 REMARK 465 THR A 64 REMARK 465 GLN A 65 REMARK 465 GLN A 66 REMARK 465 VAL A 67 REMARK 465 SER A 68 REMARK 465 GLU A 69 REMARK 465 LEU A 70 REMARK 465 LYS A 71 REMARK 465 SER A 72 REMARK 465 THR A 73 REMARK 465 ASP A 74 REMARK 465 VAL A 75 REMARK 465 LYS A 76 REMARK 465 GLU A 77 REMARK 465 GLN A 78 REMARK 465 VAL A 79 REMARK 465 VAL A 80 REMARK 465 THR A 81 REMARK 465 PRO A 82 REMARK 465 TRP A 83 REMARK 465 ASP A 84 REMARK 465 VAL A 85 REMARK 465 GLU A 86 REMARK 465 GLY A 87 REMARK 465 GLY A 88 REMARK 465 VAL A 89 REMARK 465 ASP A 90 REMARK 465 GLU A 91 REMARK 465 GLN A 92 REMARK 465 GLY A 93 REMARK 465 ARG A 94 REMARK 465 ALA A 95 REMARK 465 GLN A 96 REMARK 465 ASN A 97 REMARK 465 ILE A 98 REMARK 465 SER A 345 REMARK 465 THR A 346 REMARK 465 THR A 347 REMARK 465 LYS A 348 REMARK 465 MET A 349 REMARK 465 SER A 350 REMARK 465 ALA A 351 REMARK 465 SER A 352 REMARK 465 PRO A 478 REMARK 465 LYS A 479 REMARK 465 THR A 480 REMARK 465 LYS A 481 REMARK 465 GLN A 482 REMARK 465 GLU A 483 REMARK 465 LYS A 484 REMARK 465 LYS A 485 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 LYS A 102 CG CD CE NZ REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 GLN A 106 CG CD OE1 NE2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 ASP A 167 CG OD1 OD2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 ARG A 337 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 354 CG OD1 OD2 REMARK 470 LYS A 365 CG CD CE NZ REMARK 470 LYS A 369 CG CD CE NZ REMARK 470 LYS A 373 CG CD CE NZ REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 GLU A 469 CG CD OE1 OE2 REMARK 470 LYS A 470 CG CD CE NZ REMARK 470 LYS A 477 CG CD CE NZ 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 O1 PG4 A 950 O HOH A 515 1.64 REMARK 500 O HOH A 707 O HOH A 785 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 252 O HOH A 563 7466 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 A 252 NE - CZ - NH1 ANGL. DEV. = 5.8 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 408 90.80 -161.73 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 PG4 A 950 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 951 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 952 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 953 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O5T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE AMINOACYLATION CATALYTIC FRAGMENT OF HUMAN REMARK 900 TRYPTOPHANYL-TRNA SYNTHETASE REMARK 900 RELATED ID: YOL097C RELATED DB: TARGETDB DBREF 2IP1 A 54 485 UNP Q12109 SYWC_YEAST 1 432 SEQRES 1 A 432 MET SER ASN ASP GLU THR VAL GLU LYS VAL THR GLN GLN SEQRES 2 A 432 VAL SER GLU LEU LYS SER THR ASP VAL LYS GLU GLN VAL SEQRES 3 A 432 VAL THR PRO TRP ASP VAL GLU GLY GLY VAL ASP GLU GLN SEQRES 4 A 432 GLY ARG ALA GLN ASN ILE ASP TYR ASP LYS LEU ILE LYS SEQRES 5 A 432 GLN PHE GLY THR LYS PRO VAL ASN GLU GLU THR LEU LYS SEQRES 6 A 432 ARG PHE LYS GLN VAL THR GLY ARG GLU PRO HIS HIS PHE SEQRES 7 A 432 LEU ARG LYS GLY LEU PHE PHE SER GLU ARG ASP PHE THR SEQRES 8 A 432 LYS ILE LEU ASP LEU TYR GLU GLN GLY LYS PRO PHE PHE SEQRES 9 A 432 LEU TYR THR GLY ARG GLY PRO SER SER ASP SER MET HIS SEQRES 10 A 432 LEU GLY HIS MET ILE PRO PHE VAL PHE THR LYS TRP LEU SEQRES 11 A 432 GLN GLU VAL PHE ASP VAL PRO LEU VAL ILE GLU LEU THR SEQRES 12 A 432 ASP ASP GLU LYS PHE LEU PHE LYS HIS LYS LEU THR ILE SEQRES 13 A 432 ASN ASP VAL LYS ASN PHE ALA ARG GLU ASN ALA LYS ASP SEQRES 14 A 432 ILE ILE ALA VAL GLY PHE ASP PRO LYS ASN THR PHE ILE SEQRES 15 A 432 PHE SER ASP LEU GLN TYR MET GLY GLY ALA PHE TYR GLU SEQRES 16 A 432 THR VAL VAL ARG VAL SER ARG GLN ILE THR GLY SER THR SEQRES 17 A 432 ALA LYS ALA VAL PHE GLY PHE ASN ASP SER ASP CYS ILE SEQRES 18 A 432 GLY LYS PHE HIS PHE ALA SER ILE GLN ILE ALA THR ALA SEQRES 19 A 432 PHE PRO SER SER PHE PRO ASN VAL LEU GLY LEU PRO ASP SEQRES 20 A 432 LYS THR PRO CYS LEU ILE PRO CYS ALA ILE ASP GLN ASP SEQRES 21 A 432 PRO TYR PHE ARG VAL CYS ARG ASP VAL ALA ASP LYS LEU SEQRES 22 A 432 LYS TYR SER LYS PRO ALA LEU LEU HIS SER ARG PHE PHE SEQRES 23 A 432 PRO ALA LEU GLN GLY SER THR THR LYS MET SER ALA SER SEQRES 24 A 432 ASP ASP THR THR ALA ILE PHE MET THR ASP THR PRO LYS SEQRES 25 A 432 GLN ILE GLN LYS LYS ILE ASN LYS TYR ALA PHE SER GLY SEQRES 26 A 432 GLY GLN VAL SER ALA ASP LEU HIS ARG GLU LEU GLY GLY SEQRES 27 A 432 ASN PRO ASP VAL ASP VAL ALA TYR GLN TYR LEU SER PHE SEQRES 28 A 432 PHE LYS ASP ASP ASP VAL PHE LEU LYS GLU CYS TYR ASP SEQRES 29 A 432 LYS TYR LYS SER GLY GLU LEU LEU SER GLY GLU MET LYS SEQRES 30 A 432 LYS LEU CYS ILE GLU THR LEU GLN GLU PHE VAL LYS ALA SEQRES 31 A 432 PHE GLN GLU ARG ARG ALA GLN VAL ASP GLU GLU THR LEU SEQRES 32 A 432 ASP LYS PHE MET VAL PRO HIS LYS LEU VAL TRP GLY GLU SEQRES 33 A 432 LYS GLU ARG LEU VAL ALA PRO LYS PRO LYS THR LYS GLN SEQRES 34 A 432 GLU LYS LYS HET PG4 A 950 13 HET PG4 A 951 13 HET PG4 A 952 13 HET PG4 A 953 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 PG4 4(C8 H18 O5) FORMUL 6 HOH *358(H2 O) HELIX 1 1 ASP A 99 GLY A 108 1 10 HELIX 2 2 ASN A 113 GLY A 125 1 13 HELIX 3 3 HIS A 129 LYS A 134 1 6 HELIX 4 4 ASP A 142 GLY A 153 1 12 HELIX 5 5 HIS A 170 GLY A 172 5 3 HELIX 6 6 HIS A 173 ASP A 188 1 16 HELIX 7 7 THR A 196 LYS A 204 1 9 HELIX 8 8 THR A 208 ALA A 225 1 18 HELIX 9 9 ASP A 229 LYS A 231 5 3 HELIX 10 10 ASP A 238 MET A 242 1 5 HELIX 11 11 GLY A 243 ARG A 255 1 13 HELIX 12 12 THR A 258 VAL A 265 1 8 HELIX 13 13 CYS A 273 PHE A 279 1 7 HELIX 14 14 PHE A 279 THR A 286 1 8 HELIX 15 15 ALA A 287 PHE A 292 5 6 HELIX 16 16 GLN A 312 LYS A 327 1 16 HELIX 17 17 ASP A 353 ALA A 357 5 5 HELIX 18 18 THR A 363 ALA A 375 1 13 HELIX 19 19 SER A 382 GLY A 390 1 9 HELIX 20 20 ASP A 396 LYS A 406 1 11 HELIX 21 21 ASP A 408 SER A 421 1 14 HELIX 22 22 LEU A 425 GLN A 450 1 26 HELIX 23 23 ASP A 452 VAL A 461 1 10 SHEET 1 A 7 LYS A 110 PRO A 111 0 SHEET 2 A 7 PHE A 137 ARG A 141 -1 O GLU A 140 N LYS A 110 SHEET 3 A 7 ALA A 332 SER A 336 -1 O LEU A 333 N ARG A 141 SHEET 4 A 7 CYS A 304 ALA A 309 1 N CYS A 308 O LEU A 334 SHEET 5 A 7 PHE A 157 ARG A 162 1 N PHE A 157 O LEU A 305 SHEET 6 A 7 LEU A 191 LEU A 195 1 O VAL A 192 N LEU A 158 SHEET 7 A 7 THR A 233 SER A 237 1 O PHE A 236 N LEU A 195 SITE 1 AC1 10 TYR A 159 GLY A 163 THR A 196 GLU A 199 SITE 2 AC1 10 GLN A 312 TYR A 315 HOH A 515 HOH A 576 SITE 3 AC1 10 HOH A 721 HOH A 792 SITE 1 AC2 5 TYR A 399 ASP A 409 TYR A 416 HOH A 738 SITE 2 AC2 5 HOH A 767 SITE 1 AC3 10 GLN A 240 TYR A 241 GLY A 243 GLY A 244 SITE 2 AC3 10 ALA A 245 PHE A 246 GLU A 248 PRO A 293 SITE 3 AC3 10 HOH A 505 HOH A 611 SITE 1 AC4 5 PHE A 411 GLU A 414 LYS A 418 GLU A 423 SITE 2 AC4 5 HOH A 713 CRYST1 56.350 56.350 313.640 90.00 90.00 90.00 P 43 21 2 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 0.017746 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003188 0.00000