HEADER LIGASE 28-NOV-13 4CH5 TITLE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED TITLE 2 PROPIONYL LYSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 185-454; COMPND 5 SYNONYM: PYRROLYSINE--TRNA(PYL) LIGASE, PYRROLYSYL-TRNA SYNTHETASE, COMPND 6 PYLRS; COMPND 7 EC: 6.1.1.26; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 192952; SOURCE 4 STRAIN: GO1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS LIGASE, NON-NATURAL AMINO ACID, PYRROLYSINE EXPDTA X-RAY DIFFRACTION AUTHOR V.FLUEGEL,M.VRABEL,S.SCHNEIDER REVDAT 4 20-DEC-23 4CH5 1 REMARK LINK REVDAT 3 04-MAR-20 4CH5 1 REMARK REVDAT 2 07-MAY-14 4CH5 1 JRNL REVDAT 1 19-MAR-14 4CH5 0 JRNL AUTH V.FLUGEL,M.VRABEL,S.SCHNEIDER JRNL TITL STRUCTURAL BASIS FOR THE SITE-SPECIFIC INCORPORATION OF JRNL TITL 2 LYSINE DERIVATIVES INTO PROTEINS. JRNL REF PLOS ONE V. 9 96198 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24760130 JRNL DOI 10.1371/JOURNAL.PONE.0096198 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21491 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1159 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1499 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.88000 REMARK 3 B12 (A**2) : -0.27000 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): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.877 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2227 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2128 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3006 ; 1.439 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4895 ; 0.755 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 6.626 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;33.624 ;23.491 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 392 ;14.223 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.958 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2474 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 507 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1063 ; 2.047 ; 3.081 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1063 ; 2.045 ; 3.081 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1326 ; 3.402 ; 4.594 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1164 ; 2.538 ; 3.197 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 10 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 188 A 207 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0025 103.8991 -7.3101 REMARK 3 T TENSOR REMARK 3 T11: 0.1009 T22: 0.0899 REMARK 3 T33: 0.2243 T12: 0.0189 REMARK 3 T13: -0.0980 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 6.1056 L22: 7.5107 REMARK 3 L33: 5.1575 L12: 0.8894 REMARK 3 L13: -0.5920 L23: 3.3347 REMARK 3 S TENSOR REMARK 3 S11: 0.2875 S12: -0.0718 S13: -0.4063 REMARK 3 S21: 0.3511 S22: -0.0289 S23: -0.5825 REMARK 3 S31: 0.3092 S32: 0.5459 S33: -0.2587 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 212 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5091 104.1949 -0.8263 REMARK 3 T TENSOR REMARK 3 T11: 0.2249 T22: 0.0614 REMARK 3 T33: 0.0803 T12: -0.0753 REMARK 3 T13: -0.0467 T23: 0.0607 REMARK 3 L TENSOR REMARK 3 L11: 2.4231 L22: 14.7848 REMARK 3 L33: 8.7000 L12: -2.0366 REMARK 3 L13: -1.4187 L23: 8.1375 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: -0.2051 S13: -0.2004 REMARK 3 S21: 1.3674 S22: -0.0857 S23: 0.3574 REMARK 3 S31: 1.0510 S32: -0.0387 S33: 0.0772 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 232 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): 25.2449 128.0712 5.7452 REMARK 3 T TENSOR REMARK 3 T11: 0.2876 T22: 0.2009 REMARK 3 T33: 0.2254 T12: -0.0463 REMARK 3 T13: -0.0112 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 10.0823 L22: 4.7608 REMARK 3 L33: 0.6835 L12: 6.8520 REMARK 3 L13: 0.2405 L23: 0.4009 REMARK 3 S TENSOR REMARK 3 S11: 0.1525 S12: -0.0658 S13: -0.2335 REMARK 3 S21: 0.2599 S22: -0.0430 S23: -0.1828 REMARK 3 S31: 0.2576 S32: 0.0882 S33: -0.1095 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 254 A 277 REMARK 3 ORIGIN FOR THE GROUP (A): 36.8736 143.2444 -8.6885 REMARK 3 T TENSOR REMARK 3 T11: 0.0767 T22: 0.1091 REMARK 3 T33: 0.1159 T12: -0.0804 REMARK 3 T13: 0.0097 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.4750 L22: 1.9347 REMARK 3 L33: 3.2700 L12: 0.0353 REMARK 3 L13: -0.2346 L23: -0.0429 REMARK 3 S TENSOR REMARK 3 S11: 0.0321 S12: 0.0960 S13: 0.0410 REMARK 3 S21: -0.1365 S22: 0.0340 S23: -0.2105 REMARK 3 S31: -0.0615 S32: 0.1808 S33: -0.0662 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 278 A 292 REMARK 3 ORIGIN FOR THE GROUP (A): 37.7167 135.5761 -23.8488 REMARK 3 T TENSOR REMARK 3 T11: 0.3452 T22: 0.2993 REMARK 3 T33: 0.1265 T12: -0.0805 REMARK 3 T13: 0.1060 T23: -0.1070 REMARK 3 L TENSOR REMARK 3 L11: 13.8761 L22: 9.8042 REMARK 3 L33: 2.7474 L12: -1.1249 REMARK 3 L13: -3.9757 L23: -1.1565 REMARK 3 S TENSOR REMARK 3 S11: 0.3110 S12: 0.6134 S13: -0.2074 REMARK 3 S21: -0.9794 S22: -0.1359 S23: -0.6288 REMARK 3 S31: -0.1090 S32: 0.2923 S33: -0.1750 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 293 A 343 REMARK 3 ORIGIN FOR THE GROUP (A): 37.5737 140.6279 -9.4719 REMARK 3 T TENSOR REMARK 3 T11: 0.0572 T22: 0.1180 REMARK 3 T33: 0.0821 T12: -0.0754 REMARK 3 T13: 0.0148 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.9291 L22: 2.4394 REMARK 3 L33: 1.6815 L12: 1.0717 REMARK 3 L13: 0.5356 L23: 0.5941 REMARK 3 S TENSOR REMARK 3 S11: -0.1061 S12: 0.1791 S13: -0.0721 REMARK 3 S21: -0.1774 S22: 0.1155 S23: -0.2651 REMARK 3 S31: -0.0727 S32: 0.1704 S33: -0.0094 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 344 A 360 REMARK 3 ORIGIN FOR THE GROUP (A): 48.8843 139.2579 0.1480 REMARK 3 T TENSOR REMARK 3 T11: 0.0829 T22: 0.2088 REMARK 3 T33: 0.1475 T12: -0.0557 REMARK 3 T13: -0.0226 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 7.9906 L22: 1.0781 REMARK 3 L33: 2.0917 L12: 1.8435 REMARK 3 L13: 0.7989 L23: -0.6056 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: -0.0101 S13: -0.1117 REMARK 3 S21: 0.0914 S22: -0.0941 S23: -0.2467 REMARK 3 S31: -0.1924 S32: 0.5068 S33: 0.0737 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 361 A 389 REMARK 3 ORIGIN FOR THE GROUP (A): 48.1388 128.9445 1.5778 REMARK 3 T TENSOR REMARK 3 T11: 0.0447 T22: 0.1700 REMARK 3 T33: 0.2159 T12: -0.0017 REMARK 3 T13: -0.0575 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 4.0748 L22: 5.1808 REMARK 3 L33: 5.4996 L12: 1.0056 REMARK 3 L13: -0.6827 L23: -1.9891 REMARK 3 S TENSOR REMARK 3 S11: 0.0305 S12: 0.3266 S13: -0.2662 REMARK 3 S21: -0.1907 S22: -0.0630 S23: -0.5047 REMARK 3 S31: 0.1562 S32: 0.2260 S33: 0.0325 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 390 A 413 REMARK 3 ORIGIN FOR THE GROUP (A): 48.7174 136.3694 -8.8433 REMARK 3 T TENSOR REMARK 3 T11: 0.2493 T22: 0.3475 REMARK 3 T33: 0.2610 T12: -0.0086 REMARK 3 T13: 0.0617 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 1.5999 L22: 5.3809 REMARK 3 L33: 1.6651 L12: 0.5580 REMARK 3 L13: 0.6816 L23: -2.1483 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: 0.3541 S13: 0.0064 REMARK 3 S21: -0.3519 S22: -0.2226 S23: -0.3876 REMARK 3 S31: -0.0082 S32: 0.3410 S33: 0.1816 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 414 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 32.9220 125.2517 -4.1621 REMARK 3 T TENSOR REMARK 3 T11: 0.0467 T22: 0.0470 REMARK 3 T33: 0.0393 T12: -0.0238 REMARK 3 T13: -0.0054 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 2.9239 L22: 2.1463 REMARK 3 L33: 1.3365 L12: 1.3691 REMARK 3 L13: 0.6513 L23: 0.0352 REMARK 3 S TENSOR REMARK 3 S11: -0.0036 S12: 0.1365 S13: -0.2741 REMARK 3 S21: -0.0059 S22: 0.1073 S23: -0.1566 REMARK 3 S31: 0.1266 S32: 0.0581 S33: -0.1037 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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. U VALUES WITH TLS ADDED. RESIDUES 380-383 DISORDERED REMARK 4 REMARK 4 4CH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1290059060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22651 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 42.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 4BWA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LIAC, 14% PEG3350, PH 7.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 23.60033 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 47.20067 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.60033 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 47.20067 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 52.68800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 273.77488 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 164 REMARK 465 GLY A 165 REMARK 465 SER A 166 REMARK 465 SER A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 SER A 174 REMARK 465 SER A 175 REMARK 465 GLY A 176 REMARK 465 LEU A 177 REMARK 465 VAL A 178 REMARK 465 PRO A 179 REMARK 465 ARG A 180 REMARK 465 GLY A 181 REMARK 465 SER A 182 REMARK 465 HIS A 183 REMARK 465 MET A 184 REMARK 465 ALA A 185 REMARK 465 SER A 186 REMARK 465 ALA A 187 REMARK 465 SER A 380 REMARK 465 CYS A 381 REMARK 465 MET A 382 REMARK 465 VAL A 383 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 205 CG CD CE NZ REMARK 470 GLU A 207 CG CD OE1 OE2 REMARK 470 ASN A 211 CG OD1 ND2 REMARK 470 ARG A 217 NE CZ NH1 NH2 REMARK 470 LYS A 229 CD CE NZ REMARK 470 ASP A 281 CG OD1 OD2 REMARK 470 THR A 282 OG1 CG2 REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 ASP A 334 CG OD1 OD2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 TYR A 384 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 435 CG CD CE NZ 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 LYS A 205 34.98 71.06 REMARK 500 GLU A 237 -76.54 -110.63 REMARK 500 ASP A 292 -156.82 -115.12 REMARK 500 ASP A 334 -77.29 -51.58 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 MG A1455 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE2 REMARK 620 2 YLP A 500 OAF 71.9 REMARK 620 3 POP A1461 O3 69.0 76.5 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 YLP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1455 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1456 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1457 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1458 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1459 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 1461 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CH3 RELATED DB: PDB REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED REMARK 900 BUTYRYL LYSINE REMARK 900 RELATED ID: 4CH4 RELATED DB: PDB REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED REMARK 900 CROTONYL LYSINE REMARK 900 RELATED ID: 4CH6 RELATED DB: PDB REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED REMARK 900 PROPARGYLOXYCARBONYL LYSINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 21 AMINO ACIDS DISORDERED DBREF 4CH5 A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 4CH5 MET A 164 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 GLY A 165 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 SER A 166 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 SER A 167 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 168 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 169 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 170 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 171 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 172 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 173 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 SER A 174 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 SER A 175 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 GLY A 176 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 LEU A 177 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 VAL A 178 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 PRO A 179 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 ARG A 180 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH5 HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQRES 1 A 291 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 291 LEU VAL PRO ARG GLY SER HIS MET ALA SER ALA PRO ALA SEQRES 3 A 291 LEU THR LYS SER GLN THR ASP ARG LEU GLU VAL LEU LEU SEQRES 4 A 291 ASN PRO LYS ASP GLU ILE SER LEU ASN SER GLY LYS PRO SEQRES 5 A 291 PHE ARG GLU LEU GLU SER GLU LEU LEU SER ARG ARG LYS SEQRES 6 A 291 LYS ASP LEU GLN GLN ILE TYR ALA GLU GLU ARG GLU ASN SEQRES 7 A 291 TYR LEU GLY LYS LEU GLU ARG GLU ILE THR ARG PHE PHE SEQRES 8 A 291 VAL ASP ARG GLY PHE LEU GLU ILE LYS SER PRO ILE LEU SEQRES 9 A 291 ILE PRO LEU GLU TYR ILE GLU ARG MET GLY ILE ASP ASN SEQRES 10 A 291 ASP THR GLU LEU SER LYS GLN ILE PHE ARG VAL ASP LYS SEQRES 11 A 291 ASN PHE CYS LEU ARG PRO MET LEU ALA PRO ASN LEU TYR SEQRES 12 A 291 ASN TYR LEU ARG LYS LEU ASP ARG ALA LEU PRO ASP PRO SEQRES 13 A 291 ILE LYS ILE PHE GLU ILE GLY PRO CYS TYR ARG LYS GLU SEQRES 14 A 291 SER ASP GLY LYS GLU HIS LEU GLU GLU PHE THR MET LEU SEQRES 15 A 291 ASN PHE CYS GLN MET GLY SER GLY CYS THR ARG GLU ASN SEQRES 16 A 291 LEU GLU SER ILE ILE THR ASP PHE LEU ASN HIS LEU GLY SEQRES 17 A 291 ILE ASP PHE LYS ILE VAL GLY ASP SER CYS MET VAL TYR SEQRES 18 A 291 GLY ASP THR LEU ASP VAL MET HIS GLY ASP LEU GLU LEU SEQRES 19 A 291 SER SER ALA VAL VAL GLY PRO ILE PRO LEU ASP ARG GLU SEQRES 20 A 291 TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA GLY PHE GLY SEQRES 21 A 291 LEU GLU ARG LEU LEU LYS VAL LYS HIS ASP PHE LYS ASN SEQRES 22 A 291 ILE LYS ARG ALA ALA ARG SER GLU SER TYR TYR ASN GLY SEQRES 23 A 291 ILE SER THR ASN LEU HET YLP A 500 36 HET MG A1455 1 HET EDO A1456 4 HET EDO A1457 4 HET EDO A1458 4 HET EDO A1459 4 HET EDO A1460 4 HET POP A1461 9 HETNAM YLP (S)-2-AMINO-6-PROPIONAMIDOHEXANOIC(((2R,3S,4R,5R)-5-(6- HETNAM 2 YLP AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- HETNAM 3 YLP YL)METHYL PHOSPHORIC) ANHYDRIDE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM POP PYROPHOSPHATE 2- HETSYN EDO ETHYLENE GLYCOL FORMUL 2 YLP C19 H30 N7 O9 P FORMUL 3 MG MG 2+ FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 POP H2 O7 P2 2- FORMUL 10 HOH *89(H2 O) HELIX 1 1 THR A 191 LEU A 202 1 12 HELIX 2 2 PRO A 215 GLU A 237 1 23 HELIX 3 3 ASN A 241 ARG A 257 1 17 HELIX 4 4 LEU A 270 MET A 276 1 7 HELIX 5 5 THR A 282 GLN A 287 1 6 HELIX 6 6 LEU A 301 ASP A 313 1 13 HELIX 7 7 THR A 355 GLY A 371 1 17 HELIX 8 8 ILE A 405 GLY A 412 5 8 HELIX 9 9 LEU A 424 ASP A 433 1 10 HELIX 10 10 ASN A 436 ALA A 441 5 6 SHEET 1 AA 7 LEU A 260 ILE A 262 0 SHEET 2 AA 7 ILE A 320 TYR A 329 1 O LYS A 321 N LEU A 260 SHEET 3 AA 7 GLU A 341 MET A 350 -1 O PHE A 342 N CYS A 328 SHEET 4 AA 7 TRP A 417 GLY A 423 -1 O ILE A 418 N GLN A 349 SHEET 5 AA 7 LEU A 395 VAL A 402 -1 O LEU A 397 N GLY A 423 SHEET 6 AA 7 THR A 387 HIS A 392 -1 O LEU A 388 N ALA A 400 SHEET 7 AA 7 LYS A 375 VAL A 377 -1 O LYS A 375 N MET A 391 SHEET 1 AB 2 LEU A 267 PRO A 269 0 SHEET 2 AB 2 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 1 AC 2 TYR A 446 TYR A 447 0 SHEET 2 AC 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447 LINK OE2 GLU A 396 MG MG A1455 1555 1555 2.88 LINK OAF YLP A 500 MG MG A1455 1555 1555 2.22 LINK MG MG A1455 O3 POP A1461 1555 1555 2.73 CISPEP 1 ASP A 318 PRO A 319 0 -1.25 CISPEP 2 GLY A 403 PRO A 404 0 -1.60 SITE 1 AC1 19 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC1 19 PHE A 342 MET A 344 ASN A 346 GLU A 396 SITE 3 AC1 19 LEU A 397 SER A 398 SER A 399 TRP A 417 SITE 4 AC1 19 GLY A 421 GLY A 423 ARG A 426 MG A1455 SITE 5 AC1 19 POP A1461 HOH A2047 HOH A2081 SITE 1 AC2 4 GLU A 396 SER A 399 YLP A 500 POP A1461 SITE 1 AC3 5 TYR A 242 LYS A 245 GLU A 249 LYS A 431 SITE 2 AC3 5 HIS A 432 SITE 1 AC4 5 ASP A 313 GLY A 412 ASP A 414 LYS A 415 SITE 2 AC4 5 HOH A2049 SITE 1 AC5 7 ASN A 241 ARG A 439 ALA A 440 ALA A 441 SITE 2 AC5 7 ASN A 448 GLY A 449 HOH A2083 SITE 1 AC6 4 TYR A 272 ASN A 307 ARG A 310 LYS A 311 SITE 1 AC7 3 ASP A 373 LYS A 375 GLY A 393 SITE 1 AC8 7 ARG A 330 GLU A 332 HIS A 338 GLU A 396 SITE 2 AC8 7 ARG A 426 YLP A 500 MG A1455 CRYST1 105.376 105.376 70.801 90.00 90.00 120.00 P 64 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 0.009490 0.005479 0.000000 0.00000 SCALE2 0.000000 0.010958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014124 0.00000