HEADER LIGASE 29-FEB-16 5IHX TITLE CRYSTAL STRUCTURE OF A C-TERMINALLY TRUNCATED ASPERGILLUS NIDULANS TITLE 2 MITOCHONDRIAL TYROSYL-TRNA SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE--TRNA LIGASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TYROSYL-TRNA SYNTHETASE; COMPND 5 EC: 6.1.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EMERICELLA NIDULANS; SOURCE 3 ORGANISM_COMMON: ASPERGILLUS NIDULANS; SOURCE 4 ORGANISM_TAXID: 227321; SOURCE 5 STRAIN: R153; SOURCE 6 GENE: AN1709.2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS TRNA AMINOACYLATION, ATP-BINDING, TYROSINE-TRNA LIGASE, NUCLEOTIDE- KEYWDS 2 BINDING MOTIF, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.T.LAMECH,A.M.LAMBOWITZ REVDAT 4 27-SEP-23 5IHX 1 REMARK REVDAT 3 25-DEC-19 5IHX 1 REMARK REVDAT 2 27-SEP-17 5IHX 1 REMARK REVDAT 1 06-APR-16 5IHX 0 JRNL AUTH L.T.LAMECH,M.SAOJI,P.J.PAUKSTELIS,A.M.LAMBOWITZ JRNL TITL CRYSTAL STRUCTURE OF A C-TERMINALLY TRUNCATED ASPERGILLUS JRNL TITL 2 NIDULANS MITOCHONDRIAL TYROSYL-TRNA SYNTHETASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1535 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 43879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2210 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.0288 - 5.7873 1.00 2792 157 0.1936 0.1991 REMARK 3 2 5.7873 - 4.5949 1.00 2703 128 0.1839 0.2163 REMARK 3 3 4.5949 - 4.0145 1.00 2668 126 0.1614 0.1751 REMARK 3 4 4.0145 - 3.6476 1.00 2629 129 0.1659 0.2221 REMARK 3 5 3.6476 - 3.3862 1.00 2642 141 0.1681 0.2072 REMARK 3 6 3.3862 - 3.1866 1.00 2586 145 0.1795 0.1886 REMARK 3 7 3.1866 - 3.0271 1.00 2611 126 0.1719 0.2271 REMARK 3 8 3.0271 - 2.8953 1.00 2591 142 0.1766 0.2196 REMARK 3 9 2.8953 - 2.7839 1.00 2577 149 0.1906 0.2660 REMARK 3 10 2.7839 - 2.6878 1.00 2588 144 0.1891 0.2503 REMARK 3 11 2.6878 - 2.6038 1.00 2587 142 0.1878 0.2368 REMARK 3 12 2.6038 - 2.5294 1.00 2592 139 0.1898 0.2318 REMARK 3 13 2.5294 - 2.4628 1.00 2565 140 0.1868 0.2420 REMARK 3 14 2.4628 - 2.4027 1.00 2567 144 0.1950 0.2400 REMARK 3 15 2.4027 - 2.3481 1.00 2594 126 0.1963 0.2962 REMARK 3 16 2.3481 - 2.2981 0.93 2377 132 0.2189 0.2629 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.46 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 5563 REMARK 3 ANGLE : 0.720 7550 REMARK 3 CHIRALITY : 0.028 822 REMARK 3 PLANARITY : 0.003 967 REMARK 3 DIHEDRAL : 11.551 1958 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -42.6421 -1.6742 -14.2909 REMARK 3 T TENSOR REMARK 3 T11: 0.2343 T22: 0.2279 REMARK 3 T33: 0.2105 T12: 0.0080 REMARK 3 T13: 0.0180 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.4293 L22: 0.4094 REMARK 3 L33: 0.2783 L12: -0.0150 REMARK 3 L13: 0.1683 L23: 0.0754 REMARK 3 S TENSOR REMARK 3 S11: 0.0213 S12: 0.0207 S13: 0.0002 REMARK 3 S21: -0.1202 S22: -0.0044 S23: -0.0589 REMARK 3 S31: -0.0791 S32: -0.0094 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IHX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218833. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-12 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44001 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.298 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.72400 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: PHASER 2.5.0 REMARK 200 STARTING MODEL: 3TS1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM TRIS-HCL PH 8.5, 8% PEG 8000, 1 REMARK 280 MM L-TYROSINE, 12% GLYCEROL, VAPOR DIFFUSION, TEMPERATURE 295K 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 34.73050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.12350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.12350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.73050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.47500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 34.73050 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 42.47500 REMARK 350 BIOMT3 2 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 59 REMARK 465 GLY A 60 REMARK 465 GLN A 61 REMARK 465 GLN A 62 REMARK 465 ARG A 63 REMARK 465 TRP A 64 REMARK 465 ILE A 65 REMARK 465 THR A 66 REMARK 465 GLN A 67 REMARK 465 ALA A 68 REMARK 465 TYR A 69 REMARK 465 LEU A 70 REMARK 465 GLN A 71 REMARK 465 ARG A 72 REMARK 465 SER A 346 REMARK 465 GLY A 347 REMARK 465 GLU A 348 REMARK 465 LYS A 349 REMARK 465 PHE A 350 REMARK 465 GLY A 351 REMARK 465 LYS A 352 REMARK 465 SER A 353 REMARK 465 ALA A 354 REMARK 465 GLY A 355 REMARK 465 ARG A 443 REMARK 465 PRO A 444 REMARK 465 ARG A 445 REMARK 465 THR A 446 REMARK 465 SER A 447 REMARK 465 THR A 448 REMARK 465 ALA A 449 REMARK 465 GLU A 450 REMARK 465 PRO A 451 REMARK 465 THR A 452 REMARK 465 PRO A 453 REMARK 465 MET B 59 REMARK 465 GLY B 60 REMARK 465 GLN B 61 REMARK 465 GLN B 62 REMARK 465 ARG B 63 REMARK 465 TRP B 64 REMARK 465 ILE B 65 REMARK 465 THR B 66 REMARK 465 GLN B 67 REMARK 465 ALA B 68 REMARK 465 TYR B 69 REMARK 465 LEU B 70 REMARK 465 ARG B 168 REMARK 465 VAL B 169 REMARK 465 GLY B 170 REMARK 465 ASP B 171 REMARK 465 PRO B 172 REMARK 465 THR B 173 REMARK 465 GLY B 174 REMARK 465 ARG B 175 REMARK 465 LEU B 176 REMARK 465 LYS B 177 REMARK 465 GLY B 178 REMARK 465 ARG B 179 REMARK 465 GLU B 180 REMARK 465 GLN B 181 REMARK 465 VAL B 182 REMARK 465 MET B 262 REMARK 465 GLU B 263 REMARK 465 ARG B 264 REMARK 465 GLY B 265 REMARK 465 ASP B 266 REMARK 465 THR B 343 REMARK 465 THR B 344 REMARK 465 SER B 345 REMARK 465 SER B 346 REMARK 465 GLY B 347 REMARK 465 GLU B 348 REMARK 465 LYS B 349 REMARK 465 PHE B 350 REMARK 465 GLY B 351 REMARK 465 LYS B 352 REMARK 465 SER B 353 REMARK 465 ALA B 354 REMARK 465 GLY B 355 REMARK 465 ARG B 443 REMARK 465 PRO B 444 REMARK 465 ARG B 445 REMARK 465 THR B 446 REMARK 465 SER B 447 REMARK 465 THR B 448 REMARK 465 ALA B 449 REMARK 465 GLU B 450 REMARK 465 PRO B 451 REMARK 465 THR B 452 REMARK 465 PRO B 453 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 ILE A 73 CG1 CG2 CD1 REMARK 470 GLU A 74 CG CD OE1 OE2 REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 LYS A 78 CD CE NZ REMARK 470 LYS A 93 CE NZ REMARK 470 ARG A 168 NH1 NH2 REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 177 CG CD CE NZ REMARK 470 ARG A 179 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 GLN A 181 CG CD OE1 NE2 REMARK 470 ARG A 187 CD NE CZ NH1 NH2 REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 LYS A 215 CG CD CE NZ REMARK 470 MET A 218 CG SD CE REMARK 470 ARG A 221 NH1 NH2 REMARK 470 LYS A 233 CE NZ REMARK 470 ARG A 248 CZ NH1 NH2 REMARK 470 ARG A 255 CD NE CZ NH1 NH2 REMARK 470 ASP A 256 CG OD1 OD2 REMARK 470 LYS A 259 CD CE NZ REMARK 470 GLU A 263 CG CD OE1 OE2 REMARK 470 ARG A 264 CD NE CZ NH1 NH2 REMARK 470 ASP A 266 CG OD1 OD2 REMARK 470 LYS A 288 NZ REMARK 470 LYS A 316 CE NZ REMARK 470 LEU A 320 CG CD1 CD2 REMARK 470 GLN A 321 CG CD OE1 NE2 REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 LYS A 399 CE NZ REMARK 470 GLN A 437 CD OE1 NE2 REMARK 470 GLN A 440 CD OE1 NE2 REMARK 470 LEU A 441 CD1 CD2 REMARK 470 PHE A 442 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 71 CG CD OE1 NE2 REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 73 CG1 CG2 CD1 REMARK 470 GLU B 74 CG CD OE1 OE2 REMARK 470 GLU B 75 CG CD OE1 OE2 REMARK 470 LYS B 77 CE NZ REMARK 470 LYS B 78 CE NZ REMARK 470 GLU B 79 CD OE1 OE2 REMARK 470 GLN B 82 OE1 NE2 REMARK 470 GLN B 85 CG CD OE1 NE2 REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 LYS B 91 CG CD CE NZ REMARK 470 LYS B 93 CE NZ REMARK 470 HIS B 183 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 185 OG REMARK 470 ARG B 187 CD NE CZ NH1 NH2 REMARK 470 LYS B 188 CG CD CE NZ REMARK 470 LYS B 200 CD CE NZ REMARK 470 LYS B 215 CG CD CE NZ REMARK 470 MET B 218 CG SD CE REMARK 470 LYS B 233 CE NZ REMARK 470 ARG B 248 CD NE CZ NH1 NH2 REMARK 470 ARG B 255 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 256 CG OD1 OD2 REMARK 470 THR B 257 OG1 CG2 REMARK 470 LYS B 259 CE NZ REMARK 470 ASN B 260 OD1 ND2 REMARK 470 ARG B 261 NE CZ NH1 NH2 REMARK 470 LYS B 316 CG CD CE NZ REMARK 470 GLU B 322 CG CD OE1 OE2 REMARK 470 SER B 328 OG REMARK 470 LEU B 342 CG CD1 CD2 REMARK 470 ASN B 356 CG OD1 ND2 REMARK 470 LYS B 362 CE NZ REMARK 470 GLU B 396 OE1 OE2 REMARK 470 LYS B 399 NZ REMARK 470 GLN B 406 OE1 NE2 REMARK 470 ARG B 439 CG CD NE CZ NH1 NH2 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 HG1 THR B 166 O HOH B 501 1.58 REMARK 500 OG1 THR B 166 O HOH B 501 2.19 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 HIS A 106 -69.24 -93.95 REMARK 500 LEU A 243 -55.06 -134.66 REMARK 500 MET A 268 138.30 -171.74 REMARK 500 ASP A 407 85.36 -162.71 REMARK 500 HIS B 106 -70.73 -94.39 REMARK 500 LEU B 243 -55.01 -134.32 REMARK 500 MET B 268 142.21 -170.92 REMARK 500 ASP B 407 86.70 -165.51 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 TYR A 501 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE UNIPROT SEQUENCE FOR THIS GENE (AN1709.2) IS A PARTIAL REMARK 999 SEQUENCE. THE FIRST 132 RESIDUES CONTAIN THE MITOCHONDRIAL REMARK 999 TARGETING SEQUENCE AND ONE OF THE CONSERVED MOTIFS OF TYROSYL-TRNA REMARK 999 SYNTHETASES INVOLVED IN CHARGING TYROSINE WITH AMP. THE ASPERGILLUS REMARK 999 NIDULANS MTTYRRS SEQUENCE WAS CLONED FROM A CDNA LIBRARY WHICH REMARK 999 INCLUDES THE UPSTREAM 132 RESIDUE SEQUENCE. THE FULL-LENGTH PROTEIN REMARK 999 HAS BEEN CHARACTERIZED IN A PREVIOUS PUBLICATION: PAUKSTELIS, P. J., REMARK 999 AND LAMBOWITZ, A. M. (2008) IDENTIFICATION AND EVOLUTION OF FUNGAL REMARK 999 MITOCHONDRIAL TYROSYL-TRNA SYNTHETASES WITH GROUP I INTRON SPLICING REMARK 999 ACTIVITY. PROC. NATL. ACAD. SCI. U. S. A. 105, 6010-6015. DBREF 5IHX A 59 190 PDB 5IHX 5IHX 59 190 DBREF 5IHX A 191 453 UNP Q5BCM1 Q5BCM1_EMENI 1 263 DBREF 5IHX B 59 190 PDB 5IHX 5IHX 59 190 DBREF 5IHX B 191 453 UNP Q5BCM1 Q5BCM1_EMENI 1 263 SEQRES 1 A 395 MET GLY GLN GLN ARG TRP ILE THR GLN ALA TYR LEU GLN SEQRES 2 A 395 ARG ILE GLU GLU GLY LYS LYS GLU TRP ALA GLN PHE ALA SEQRES 3 A 395 GLN GLU ILE LYS GLU GLY LYS ARG LYS SER PHE VAL GLU SEQRES 4 A 395 HIS LEU GLU GLU ARG GLY LEU ILE HIS ASP VAL VAL GLY SEQRES 5 A 395 ASP ARG ASP LEU LEU HIS ARG VAL PHE THR GLU LYS ARG SEQRES 6 A 395 VAL GLY ILE TYR ALA GLY VAL ASP PRO THR ALA PRO SER SEQRES 7 A 395 MET HIS VAL GLY HIS MET LEU PRO PHE MET VAL LEU ALA SEQRES 8 A 395 TRP GLY TYR VAL TRP GLY LEU PRO VAL THR PHE LEU LEU SEQRES 9 A 395 GLY GLY ALA THR SER ARG VAL GLY ASP PRO THR GLY ARG SEQRES 10 A 395 LEU LYS GLY ARG GLU GLN VAL HIS SER SER VAL ARG LYS SEQRES 11 A 395 ALA ASN MET ALA SER MET HIS MET GLN LEU LYS LYS LEU SEQRES 12 A 395 GLY ALA SER ILE GLU ARG TYR GLY GLU LYS HIS GLY TYR SEQRES 13 A 395 LYS ARG GLN MET ILE TRP ARG ARG THR LEU THR ASN ASN SEQRES 14 A 395 ASN VAL TRP TRP ASN LYS THR PRO LEU LEU GLU VAL LEU SEQRES 15 A 395 ARG ASP LEU GLY ALA TYR ILE ARG ILE GLY PRO MET LEU SEQRES 16 A 395 GLY ARG ASP THR VAL LYS ASN ARG MET GLU ARG GLY ASP SEQRES 17 A 395 GLY MET SER PHE ALA GLU PHE THR TYR PRO LEU MET GLN SEQRES 18 A 395 ALA TRP ASP TRP TRP MET LEU PHE LYS ASN GLY CYS GLN SEQRES 19 A 395 VAL GLN VAL GLY GLY SER ASP GLN TYR GLY ASN ILE LEU SEQRES 20 A 395 PHE GLY VAL GLY ALA VAL LYS THR ILE SER LYS ASN THR SEQRES 21 A 395 VAL LEU GLN GLU ASP ASN ASN PRO LEU SER ASP ASP LEU SEQRES 22 A 395 ASP LYS PRO ILE GLY PHE THR THR PRO LEU LEU THR THR SEQRES 23 A 395 SER SER GLY GLU LYS PHE GLY LYS SER ALA GLY ASN ALA SEQRES 24 A 395 ILE TRP LEU ASP LYS ASP MET THR SER THR PHE GLU LEU SEQRES 25 A 395 TYR GLN PHE PHE VAL ARG THR PRO ASP ASP ALA VAL GLU SEQRES 26 A 395 ARG TYR LEU LYS MET PHE THR PHE LEU PRO ILE PRO GLU SEQRES 27 A 395 ILE SER LYS ILE MET GLU GLU GLN ASN GLN ASP PRO SER SEQRES 28 A 395 ARG ARG VAL ALA GLN HIS ALA LEU ALA TYR GLU PHE VAL SEQRES 29 A 395 GLU LEU ILE HIS GLY LYS ASP GLU ALA ASP ALA VAL SER SEQRES 30 A 395 MET GLN HIS ARG GLN LEU PHE ARG PRO ARG THR SER THR SEQRES 31 A 395 ALA GLU PRO THR PRO SEQRES 1 B 395 MET GLY GLN GLN ARG TRP ILE THR GLN ALA TYR LEU GLN SEQRES 2 B 395 ARG ILE GLU GLU GLY LYS LYS GLU TRP ALA GLN PHE ALA SEQRES 3 B 395 GLN GLU ILE LYS GLU GLY LYS ARG LYS SER PHE VAL GLU SEQRES 4 B 395 HIS LEU GLU GLU ARG GLY LEU ILE HIS ASP VAL VAL GLY SEQRES 5 B 395 ASP ARG ASP LEU LEU HIS ARG VAL PHE THR GLU LYS ARG SEQRES 6 B 395 VAL GLY ILE TYR ALA GLY VAL ASP PRO THR ALA PRO SER SEQRES 7 B 395 MET HIS VAL GLY HIS MET LEU PRO PHE MET VAL LEU ALA SEQRES 8 B 395 TRP GLY TYR VAL TRP GLY LEU PRO VAL THR PHE LEU LEU SEQRES 9 B 395 GLY GLY ALA THR SER ARG VAL GLY ASP PRO THR GLY ARG SEQRES 10 B 395 LEU LYS GLY ARG GLU GLN VAL HIS SER SER VAL ARG LYS SEQRES 11 B 395 ALA ASN MET ALA SER MET HIS MET GLN LEU LYS LYS LEU SEQRES 12 B 395 GLY ALA SER ILE GLU ARG TYR GLY GLU LYS HIS GLY TYR SEQRES 13 B 395 LYS ARG GLN MET ILE TRP ARG ARG THR LEU THR ASN ASN SEQRES 14 B 395 ASN VAL TRP TRP ASN LYS THR PRO LEU LEU GLU VAL LEU SEQRES 15 B 395 ARG ASP LEU GLY ALA TYR ILE ARG ILE GLY PRO MET LEU SEQRES 16 B 395 GLY ARG ASP THR VAL LYS ASN ARG MET GLU ARG GLY ASP SEQRES 17 B 395 GLY MET SER PHE ALA GLU PHE THR TYR PRO LEU MET GLN SEQRES 18 B 395 ALA TRP ASP TRP TRP MET LEU PHE LYS ASN GLY CYS GLN SEQRES 19 B 395 VAL GLN VAL GLY GLY SER ASP GLN TYR GLY ASN ILE LEU SEQRES 20 B 395 PHE GLY VAL GLY ALA VAL LYS THR ILE SER LYS ASN THR SEQRES 21 B 395 VAL LEU GLN GLU ASP ASN ASN PRO LEU SER ASP ASP LEU SEQRES 22 B 395 ASP LYS PRO ILE GLY PHE THR THR PRO LEU LEU THR THR SEQRES 23 B 395 SER SER GLY GLU LYS PHE GLY LYS SER ALA GLY ASN ALA SEQRES 24 B 395 ILE TRP LEU ASP LYS ASP MET THR SER THR PHE GLU LEU SEQRES 25 B 395 TYR GLN PHE PHE VAL ARG THR PRO ASP ASP ALA VAL GLU SEQRES 26 B 395 ARG TYR LEU LYS MET PHE THR PHE LEU PRO ILE PRO GLU SEQRES 27 B 395 ILE SER LYS ILE MET GLU GLU GLN ASN GLN ASP PRO SER SEQRES 28 B 395 ARG ARG VAL ALA GLN HIS ALA LEU ALA TYR GLU PHE VAL SEQRES 29 B 395 GLU LEU ILE HIS GLY LYS ASP GLU ALA ASP ALA VAL SER SEQRES 30 B 395 MET GLN HIS ARG GLN LEU PHE ARG PRO ARG THR SER THR SEQRES 31 B 395 ALA GLU PRO THR PRO HET TYR A 501 24 HETNAM TYR TYROSINE FORMUL 3 TYR C9 H11 N O3 FORMUL 4 HOH *217(H2 O) HELIX 1 AA1 ILE A 73 GLU A 89 1 17 HELIX 2 AA2 SER A 94 GLY A 103 1 10 HELIX 3 AA3 ASP A 111 LYS A 122 1 12 HELIX 4 AA4 HIS A 138 GLY A 140 5 3 HELIX 5 AA5 HIS A 141 TRP A 154 1 14 HELIX 6 AA6 ALA A 165 GLY A 170 1 6 HELIX 7 AA7 HIS A 183 HIS A 212 1 30 HELIX 8 AA8 ASN A 227 ASN A 232 1 6 HELIX 9 AA9 PRO A 235 LEU A 243 1 9 HELIX 10 AB1 GLY A 244 ILE A 247 5 4 HELIX 11 AB2 ARG A 248 ARG A 255 1 8 HELIX 12 AB3 ARG A 255 ARG A 264 1 10 HELIX 13 AB4 SER A 269 LYS A 288 1 20 HELIX 14 AB5 GLY A 297 ASP A 299 5 3 HELIX 15 AB6 GLN A 300 THR A 318 1 19 HELIX 16 AB7 ASP A 329 LYS A 333 5 5 HELIX 17 AB8 SER A 366 ARG A 376 1 11 HELIX 18 AB9 PRO A 378 THR A 390 1 13 HELIX 19 AC1 PRO A 393 ASP A 407 1 15 HELIX 20 AC2 PRO A 408 ARG A 410 5 3 HELIX 21 AC3 ARG A 411 GLY A 427 1 17 HELIX 22 AC4 GLY A 427 PHE A 442 1 16 HELIX 23 AC5 ARG B 72 GLU B 89 1 18 HELIX 24 AC6 SER B 94 GLY B 103 1 10 HELIX 25 AC7 ASP B 111 LYS B 122 1 12 HELIX 26 AC8 HIS B 138 GLY B 140 5 3 HELIX 27 AC9 HIS B 141 TRP B 154 1 14 HELIX 28 AD1 SER B 184 HIS B 212 1 29 HELIX 29 AD2 ASN B 227 ASN B 232 1 6 HELIX 30 AD3 PRO B 235 LEU B 243 1 9 HELIX 31 AD4 GLY B 244 ILE B 247 5 4 HELIX 32 AD5 ARG B 248 LEU B 253 1 6 HELIX 33 AD6 ARG B 255 ASN B 260 1 6 HELIX 34 AD7 SER B 269 LYS B 288 1 20 HELIX 35 AD8 GLY B 297 ASP B 299 5 3 HELIX 36 AD9 GLN B 300 THR B 318 1 19 HELIX 37 AE1 ASP B 329 LYS B 333 5 5 HELIX 38 AE2 SER B 366 ARG B 376 1 11 HELIX 39 AE3 ALA B 381 THR B 390 1 10 HELIX 40 AE4 PRO B 393 ASP B 407 1 15 HELIX 41 AE5 PRO B 408 ARG B 410 5 3 HELIX 42 AE6 ARG B 411 GLY B 427 1 17 HELIX 43 AE7 GLY B 427 PHE B 442 1 16 SHEET 1 AA1 6 VAL A 108 VAL A 109 0 SHEET 2 AA1 6 ILE A 335 THR A 338 -1 O GLY A 336 N VAL A 109 SHEET 3 AA1 6 VAL A 293 GLY A 296 1 N GLN A 294 O PHE A 337 SHEET 4 AA1 6 ILE A 126 VAL A 130 1 N TYR A 127 O VAL A 295 SHEET 5 AA1 6 VAL A 158 LEU A 162 1 O LEU A 161 N ALA A 128 SHEET 6 AA1 6 ARG A 222 ASN A 226 1 O THR A 223 N PHE A 160 SHEET 1 AA2 6 VAL B 108 VAL B 109 0 SHEET 2 AA2 6 ILE B 335 THR B 338 -1 O GLY B 336 N VAL B 109 SHEET 3 AA2 6 CYS B 291 GLY B 296 1 N GLN B 294 O PHE B 337 SHEET 4 AA2 6 GLY B 125 VAL B 130 1 N TYR B 127 O VAL B 295 SHEET 5 AA2 6 VAL B 158 LEU B 162 1 O LEU B 161 N ALA B 128 SHEET 6 AA2 6 ARG B 222 ASN B 226 1 O THR B 225 N LEU B 162 SITE 1 AC1 11 TYR A 127 GLY A 129 ASP A 131 LEU A 161 SITE 2 AC1 11 ASP A 171 TYR A 275 GLN A 279 ASP A 282 SITE 3 AC1 11 GLN A 294 GLN A 300 HOH A 691 CRYST1 69.461 84.950 164.247 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 0.014397 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006088 0.00000