HEADER LIGASE 28-NOV-13 4CH3 TITLE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED TITLE 2 BUTYRYL 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 3 20-DEC-23 4CH3 1 REMARK REVDAT 2 07-MAY-14 4CH3 1 JRNL REVDAT 1 19-MAR-14 4CH3 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. 2.28 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19600 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1034 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1447 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.2100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2096 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : 1.56000 REMARK 3 B12 (A**2) : -0.48000 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): 0.189 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.026 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2212 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2113 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2985 ; 1.378 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4851 ; 0.751 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 6.149 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;31.588 ;23.564 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 381 ;13.357 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.623 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2473 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 502 ; 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): 1076 ; 1.987 ; 3.197 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1076 ; 1.987 ; 3.197 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1343 ; 3.248 ; 4.775 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1136 ; 2.389 ; 3.265 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 : 11 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 206 REMARK 3 ORIGIN FOR THE GROUP (A): 24.8473 103.7189 -7.7355 REMARK 3 T TENSOR REMARK 3 T11: 0.0941 T22: 0.0812 REMARK 3 T33: 0.2221 T12: 0.0146 REMARK 3 T13: -0.1029 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 6.6659 L22: 9.3587 REMARK 3 L33: 5.5535 L12: 1.3625 REMARK 3 L13: -1.6626 L23: 3.5076 REMARK 3 S TENSOR REMARK 3 S11: 0.2729 S12: -0.1866 S13: -0.4902 REMARK 3 S21: 0.4281 S22: 0.0048 S23: -0.5758 REMARK 3 S31: 0.2075 S32: 0.5695 S33: -0.2776 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 207 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 27.2483 98.1852 -0.7658 REMARK 3 T TENSOR REMARK 3 T11: 0.4807 T22: 0.3922 REMARK 3 T33: 0.6714 T12: -0.0090 REMARK 3 T13: 0.1343 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 0.4208 L22: 24.9089 REMARK 3 L33: 1.1687 L12: -3.1310 REMARK 3 L13: 0.6745 L23: -5.2715 REMARK 3 S TENSOR REMARK 3 S11: 0.1170 S12: 0.0073 S13: -0.0307 REMARK 3 S21: 0.0336 S22: -0.1991 S23: 0.4917 REMARK 3 S31: 0.0512 S32: 0.0788 S33: 0.0821 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 214 A 239 REMARK 3 ORIGIN FOR THE GROUP (A): 17.7133 110.0205 2.0361 REMARK 3 T TENSOR REMARK 3 T11: 0.2361 T22: 0.0869 REMARK 3 T33: 0.1120 T12: -0.0647 REMARK 3 T13: -0.0228 T23: 0.0616 REMARK 3 L TENSOR REMARK 3 L11: 1.1828 L22: 14.0686 REMARK 3 L33: 6.4042 L12: -3.6545 REMARK 3 L13: -2.1466 L23: 8.3447 REMARK 3 S TENSOR REMARK 3 S11: -0.1167 S12: -0.0998 S13: -0.1090 REMARK 3 S21: 1.1425 S22: 0.0816 S23: 0.2367 REMARK 3 S31: 0.7498 S32: 0.0672 S33: 0.0351 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 240 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9039 131.4172 4.3571 REMARK 3 T TENSOR REMARK 3 T11: 0.3955 T22: 0.2366 REMARK 3 T33: 0.2367 T12: -0.0528 REMARK 3 T13: 0.0005 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 14.7356 L22: 5.9685 REMARK 3 L33: 2.7005 L12: 9.0605 REMARK 3 L13: 4.6056 L23: 2.3757 REMARK 3 S TENSOR REMARK 3 S11: 0.0869 S12: 0.2200 S13: 0.0434 REMARK 3 S21: 0.2825 S22: 0.0410 S23: 0.0724 REMARK 3 S31: 0.2248 S32: 0.0771 S33: -0.1278 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 254 A 280 REMARK 3 ORIGIN FOR THE GROUP (A): 37.3450 142.5035 -10.0445 REMARK 3 T TENSOR REMARK 3 T11: 0.0920 T22: 0.1110 REMARK 3 T33: 0.1362 T12: -0.0846 REMARK 3 T13: 0.0321 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.9700 L22: 2.1494 REMARK 3 L33: 2.9975 L12: 0.1231 REMARK 3 L13: 0.1059 L23: 0.0999 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: 0.1494 S13: 0.0061 REMARK 3 S21: -0.2117 S22: 0.0397 S23: -0.2202 REMARK 3 S31: -0.1337 S32: 0.1305 S33: -0.0243 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 281 A 329 REMARK 3 ORIGIN FOR THE GROUP (A): 38.0312 142.9088 -11.5102 REMARK 3 T TENSOR REMARK 3 T11: 0.0653 T22: 0.1027 REMARK 3 T33: 0.0833 T12: -0.0740 REMARK 3 T13: 0.0300 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 1.7660 L22: 2.6111 REMARK 3 L33: 1.7916 L12: 1.2144 REMARK 3 L13: 0.4989 L23: 0.5660 REMARK 3 S TENSOR REMARK 3 S11: -0.1540 S12: 0.1891 S13: 0.0123 REMARK 3 S21: -0.2730 S22: 0.1833 S23: -0.2626 REMARK 3 S31: -0.1439 S32: 0.2289 S33: -0.0293 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 330 A 335 REMARK 3 ORIGIN FOR THE GROUP (A): 35.8600 126.3745 -19.0511 REMARK 3 T TENSOR REMARK 3 T11: 0.6024 T22: 0.4253 REMARK 3 T33: 0.3854 T12: -0.1792 REMARK 3 T13: 0.3056 T23: -0.1959 REMARK 3 L TENSOR REMARK 3 L11: 26.0441 L22: 10.6863 REMARK 3 L33: 10.5809 L12: -4.9021 REMARK 3 L13: 11.7626 L23: -9.3757 REMARK 3 S TENSOR REMARK 3 S11: 0.7922 S12: 1.5658 S13: -1.8590 REMARK 3 S21: -1.5196 S22: -0.4967 S23: -0.4615 REMARK 3 S31: 1.2873 S32: 0.9060 S33: -0.2955 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 336 A 364 REMARK 3 ORIGIN FOR THE GROUP (A): 44.4819 134.3854 -2.7183 REMARK 3 T TENSOR REMARK 3 T11: 0.0182 T22: 0.0852 REMARK 3 T33: 0.1341 T12: -0.0140 REMARK 3 T13: 0.0047 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 3.3842 L22: 1.7203 REMARK 3 L33: 1.4041 L12: 1.5678 REMARK 3 L13: 0.5596 L23: -0.2182 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: 0.1135 S13: -0.1594 REMARK 3 S21: 0.0249 S22: -0.0368 S23: -0.2142 REMARK 3 S31: -0.0133 S32: 0.3033 S33: 0.0348 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 365 A 399 REMARK 3 ORIGIN FOR THE GROUP (A): 48.1046 126.7673 -0.9991 REMARK 3 T TENSOR REMARK 3 T11: 0.0531 T22: 0.1409 REMARK 3 T33: 0.2342 T12: 0.0110 REMARK 3 T13: -0.0304 T23: -0.0274 REMARK 3 L TENSOR REMARK 3 L11: 3.8968 L22: 4.1358 REMARK 3 L33: 3.2712 L12: -0.4819 REMARK 3 L13: 0.8510 L23: -0.0583 REMARK 3 S TENSOR REMARK 3 S11: 0.1209 S12: 0.2807 S13: -0.1195 REMARK 3 S21: -0.2806 S22: -0.0021 S23: -0.5368 REMARK 3 S31: 0.1607 S32: 0.2327 S33: -0.1189 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 400 A 418 REMARK 3 ORIGIN FOR THE GROUP (A): 51.2193 145.3791 -9.5978 REMARK 3 T TENSOR REMARK 3 T11: 0.2657 T22: 0.3549 REMARK 3 T33: 0.3034 T12: -0.1266 REMARK 3 T13: 0.0431 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 3.7594 L22: 3.8649 REMARK 3 L33: 2.3089 L12: -1.8524 REMARK 3 L13: -0.2464 L23: -2.1757 REMARK 3 S TENSOR REMARK 3 S11: 0.0939 S12: 0.3171 S13: 0.2615 REMARK 3 S21: -0.1440 S22: -0.4408 S23: -0.5965 REMARK 3 S31: -0.1862 S32: 0.3611 S33: 0.3469 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 419 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 29.8544 121.5987 -3.9768 REMARK 3 T TENSOR REMARK 3 T11: 0.0757 T22: 0.0616 REMARK 3 T33: 0.0854 T12: -0.0217 REMARK 3 T13: -0.0138 T23: -0.0409 REMARK 3 L TENSOR REMARK 3 L11: 3.3256 L22: 3.2091 REMARK 3 L33: 1.2946 L12: 1.5097 REMARK 3 L13: 0.3705 L23: -0.6315 REMARK 3 S TENSOR REMARK 3 S11: 0.0402 S12: 0.0516 S13: -0.3243 REMARK 3 S21: 0.0308 S22: 0.0457 S23: -0.1737 REMARK 3 S31: 0.2169 S32: 0.0522 S33: -0.0859 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 REMARK 4 REMARK 4 4CH3 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_1290059058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-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 : 20634 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 38.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.860 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 (%): 67.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LIAC, 12% 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 23.79400 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 47.58800 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 23.79400 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 47.58800 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 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 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 SER A 209 OG REMARK 470 ASN A 211 CG OD1 ND2 REMARK 470 SER A 212 OG REMARK 470 ARG A 217 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 229 CD CE NZ REMARK 470 GLU A 271 CG CD OE1 OE2 REMARK 470 ASP A 279 CG OD1 OD2 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 293 CG CD CE NZ REMARK 470 ASP A 334 CG OD1 OD2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 ASP A 379 CG OD1 OD2 REMARK 470 SER A 380 OG REMARK 470 CYS A 381 SG REMARK 470 MET A 382 CG SD CE REMARK 470 VAL A 383 CG1 CG2 REMARK 470 TYR A 384 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 435 CG CD CE NZ REMARK 470 LYS A 438 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 GLU A 207 70.77 49.82 REMARK 500 SER A 212 20.92 -153.75 REMARK 500 GLU A 237 -83.74 -106.83 REMARK 500 ASP A 292 -147.12 -118.72 REMARK 500 SER A 380 -71.18 -54.24 REMARK 500 TYR A 384 -73.14 -70.75 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 YLB 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 900 REMARK 900 RELATED ENTRIES 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: 4CH5 RELATED DB: PDB REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED REMARK 900 PROPIONYL 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 4CH3 A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 4CH3 MET A 164 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 GLY A 165 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 SER A 166 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 SER A 167 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 168 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 169 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 170 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 171 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 172 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 173 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 SER A 174 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 SER A 175 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 GLY A 176 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 LEU A 177 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 VAL A 178 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 PRO A 179 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 ARG A 180 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH3 MET A 184 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 YLB A 500 37 HET MG A1455 1 HET EDO A1456 4 HET EDO A1457 4 HET EDO A1458 4 HET EDO A1459 4 HET EDO A1460 4 HETNAM YLB 5'-O-({[(2R)-2-AMINO-6-(BUTANOYLAMINO) HETNAM 2 YLB HEXANOYL]OXY}PHOSPHINATO)ADENOSINE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 YLB C20 H32 N7 O9 P FORMUL 3 MG MG 2+ FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 HOH *80(H2 O) HELIX 1 1 THR A 191 LEU A 202 1 12 HELIX 2 2 ASN A 203 GLU A 207 5 5 HELIX 3 3 PRO A 215 GLU A 237 1 23 HELIX 4 4 ASN A 241 ARG A 257 1 17 HELIX 5 5 LEU A 270 MET A 276 1 7 HELIX 6 6 THR A 282 GLN A 287 1 6 HELIX 7 7 LEU A 301 ASP A 313 1 13 HELIX 8 8 THR A 355 GLY A 371 1 17 HELIX 9 9 ILE A 405 GLY A 412 5 8 HELIX 10 10 LEU A 424 ASP A 433 1 10 HELIX 11 11 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 GLY A 378 -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 OAI YLB A 500 MG MG A1455 1555 1555 2.77 CISPEP 1 ASP A 318 PRO A 319 0 -1.58 CISPEP 2 GLY A 403 PRO A 404 0 -1.13 SITE 1 AC1 18 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC1 18 PHE A 342 MET A 344 ASN A 346 GLU A 396 SITE 3 AC1 18 LEU A 397 SER A 398 SER A 399 TRP A 417 SITE 4 AC1 18 GLY A 419 GLY A 421 GLY A 423 ARG A 426 SITE 5 AC1 18 MG A1455 HOH A2070 SITE 1 AC2 2 GLU A 396 YLB A 500 SITE 1 AC3 6 TYR A 242 LYS A 245 GLU A 249 LEU A 428 SITE 2 AC3 6 LYS A 431 HIS A 432 SITE 1 AC4 6 ASN A 241 ARG A 439 ALA A 440 ASN A 448 SITE 2 AC4 6 GLY A 449 HOH A2074 SITE 1 AC5 6 ASP A 313 GLY A 412 ILE A 413 ASP A 414 SITE 2 AC5 6 LYS A 415 HOH A2046 SITE 1 AC6 4 TYR A 272 ASN A 307 ARG A 310 LYS A 311 SITE 1 AC7 5 ASP A 373 LYS A 375 MET A 391 HIS A 392 SITE 2 AC7 5 GLY A 393 CRYST1 105.257 105.257 71.382 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 0.009501 0.005485 0.000000 0.00000 SCALE2 0.000000 0.010970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014009 0.00000