HEADER LIGASE 28-NOV-13 4CH6 TITLE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED TITLE 2 PROPARGYLOXYCARBONYL 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 4CH6 1 REMARK LINK REVDAT 2 07-MAY-14 4CH6 1 JRNL REVDAT 1 19-MAR-14 4CH6 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26610 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1408 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1956 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.3110 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 : 59 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 1.80000 REMARK 3 B12 (A**2) : -0.55000 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.792 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2219 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2121 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2992 ; 1.497 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4877 ; 0.772 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 270 ; 6.388 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;34.335 ;23.491 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 390 ;14.130 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;14.293 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 327 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2467 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 506 ; 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): 1062 ; 2.300 ; 3.585 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1062 ; 2.297 ; 3.585 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1323 ; 3.531 ; 5.337 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1324 ; 3.531 ; 5.342 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1157 ; 2.680 ; 3.798 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1157 ; 2.680 ; 3.798 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1665 ; 4.093 ; 5.604 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2506 ; 7.995 ;28.450 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2507 ; 7.994 ;28.464 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 : 9 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): 24.6834 103.4398 -7.5662 REMARK 3 T TENSOR REMARK 3 T11: 0.1193 T22: 0.1225 REMARK 3 T33: 0.2955 T12: 0.0243 REMARK 3 T13: -0.1172 T23: 0.0213 REMARK 3 L TENSOR REMARK 3 L11: 5.1776 L22: 7.9977 REMARK 3 L33: 4.0975 L12: 0.7967 REMARK 3 L13: -2.2139 L23: 2.2614 REMARK 3 S TENSOR REMARK 3 S11: 0.3175 S12: -0.2597 S13: -0.3110 REMARK 3 S21: 0.5555 S22: -0.1398 S23: -0.7877 REMARK 3 S31: 0.3286 S32: 0.5549 S33: -0.1777 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): 26.6549 97.6592 0.1750 REMARK 3 T TENSOR REMARK 3 T11: 0.4136 T22: 0.4028 REMARK 3 T33: 0.4430 T12: 0.0998 REMARK 3 T13: -0.1336 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.6530 L22: 2.6000 REMARK 3 L33: 2.1427 L12: -1.2982 REMARK 3 L13: 1.1753 L23: -2.3595 REMARK 3 S TENSOR REMARK 3 S11: 0.2087 S12: 0.2959 S13: 0.2759 REMARK 3 S21: -0.4539 S22: -0.6526 S23: -0.5035 REMARK 3 S31: 0.4205 S32: 0.6087 S33: 0.4439 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): 17.3494 109.2111 1.6442 REMARK 3 T TENSOR REMARK 3 T11: 0.2431 T22: 0.1088 REMARK 3 T33: 0.1651 T12: -0.1055 REMARK 3 T13: -0.0088 T23: 0.0639 REMARK 3 L TENSOR REMARK 3 L11: 0.6961 L22: 12.1500 REMARK 3 L33: 5.3436 L12: -2.8061 REMARK 3 L13: -1.6123 L23: 7.2451 REMARK 3 S TENSOR REMARK 3 S11: -0.1737 S12: -0.1024 S13: -0.1381 REMARK 3 S21: 1.1167 S22: 0.1397 S23: 0.4574 REMARK 3 S31: 0.8158 S32: -0.0194 S33: 0.0340 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 254 REMARK 3 ORIGIN FOR THE GROUP (A): 30.5170 131.5472 4.2949 REMARK 3 T TENSOR REMARK 3 T11: 0.0391 T22: 0.0872 REMARK 3 T33: 0.0733 T12: -0.0359 REMARK 3 T13: -0.0111 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 8.4046 L22: 4.6558 REMARK 3 L33: 1.9067 L12: 4.4218 REMARK 3 L13: 1.9760 L23: 0.9150 REMARK 3 S TENSOR REMARK 3 S11: -0.0384 S12: -0.0273 S13: -0.2150 REMARK 3 S21: 0.1451 S22: 0.0624 S23: -0.1881 REMARK 3 S31: 0.0680 S32: 0.0127 S33: -0.0240 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 255 A 278 REMARK 3 ORIGIN FOR THE GROUP (A): 36.8120 142.5265 -9.8472 REMARK 3 T TENSOR REMARK 3 T11: 0.1022 T22: 0.1448 REMARK 3 T33: 0.1479 T12: -0.1104 REMARK 3 T13: 0.0235 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 1.7571 L22: 1.6176 REMARK 3 L33: 2.3361 L12: 0.0226 REMARK 3 L13: 0.2723 L23: 0.1289 REMARK 3 S TENSOR REMARK 3 S11: -0.1035 S12: 0.1074 S13: 0.0991 REMARK 3 S21: -0.2163 S22: 0.0659 S23: -0.2587 REMARK 3 S31: -0.1472 S32: 0.2164 S33: 0.0377 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 279 A 330 REMARK 3 ORIGIN FOR THE GROUP (A): 38.0811 142.0727 -11.9366 REMARK 3 T TENSOR REMARK 3 T11: 0.1131 T22: 0.1648 REMARK 3 T33: 0.1275 T12: -0.1169 REMARK 3 T13: 0.0339 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.5940 L22: 2.0709 REMARK 3 L33: 1.6856 L12: 0.3117 REMARK 3 L13: 0.1187 L23: 0.2159 REMARK 3 S TENSOR REMARK 3 S11: -0.1609 S12: 0.2342 S13: 0.0401 REMARK 3 S21: -0.3455 S22: 0.1631 S23: -0.2504 REMARK 3 S31: -0.1309 S32: 0.2609 S33: -0.0022 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 331 A 359 REMARK 3 ORIGIN FOR THE GROUP (A): 42.3420 133.2860 -6.0099 REMARK 3 T TENSOR REMARK 3 T11: 0.0429 T22: 0.1385 REMARK 3 T33: 0.1243 T12: -0.0580 REMARK 3 T13: 0.0500 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 3.5016 L22: 1.7141 REMARK 3 L33: 1.5699 L12: 1.2125 REMARK 3 L13: 0.9620 L23: -0.0990 REMARK 3 S TENSOR REMARK 3 S11: -0.1353 S12: 0.1115 S13: -0.1748 REMARK 3 S21: -0.1525 S22: 0.0847 S23: -0.2506 REMARK 3 S31: -0.0195 S32: 0.2627 S33: 0.0506 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 360 A 399 REMARK 3 ORIGIN FOR THE GROUP (A): 47.6797 127.1563 -0.0708 REMARK 3 T TENSOR REMARK 3 T11: 0.0394 T22: 0.1652 REMARK 3 T33: 0.2379 T12: -0.0118 REMARK 3 T13: -0.0040 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 2.0255 L22: 3.9165 REMARK 3 L33: 2.2128 L12: 0.3420 REMARK 3 L13: 0.5519 L23: -0.9975 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: 0.2178 S13: -0.2912 REMARK 3 S21: -0.2791 S22: 0.0252 S23: -0.4769 REMARK 3 S31: 0.2050 S32: 0.2329 S33: -0.0254 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 400 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 37.3836 129.7189 -5.9472 REMARK 3 T TENSOR REMARK 3 T11: 0.0741 T22: 0.0891 REMARK 3 T33: 0.0894 T12: -0.0452 REMARK 3 T13: 0.0292 T23: -0.0432 REMARK 3 L TENSOR REMARK 3 L11: 1.9359 L22: 2.1343 REMARK 3 L33: 1.2703 L12: 0.7465 REMARK 3 L13: 0.4053 L23: -0.1428 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: 0.1928 S13: -0.1700 REMARK 3 S21: -0.1367 S22: 0.0765 S23: -0.2625 REMARK 3 S31: -0.0402 S32: 0.1660 S33: -0.0301 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 REMARK 4 REMARK 4 4CH6 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_1290059062. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-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 : 28018 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 38.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.290 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 (%): 67.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.76 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 23.65467 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 47.30933 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 23.65467 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 47.30933 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 465 SER A 333 REMARK 465 ASP A 334 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 CD CE NZ REMARK 470 LYS A 229 CD CE NZ REMARK 470 GLN A 233 OE1 NE2 REMARK 470 GLU A 271 CD OE1 OE2 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 CE NZ REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 LYS A 375 CD CE NZ REMARK 470 ASP A 379 CG OD1 OD2 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 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 LEU A 210 36.34 -90.86 REMARK 500 ASN A 211 31.89 -163.20 REMARK 500 GLU A 237 -86.34 -108.41 REMARK 500 ASP A 292 -150.17 -121.41 REMARK 500 ASP A 414 38.97 -144.03 REMARK 500 ASP A 414 40.20 -144.64 REMARK 500 ASN A 453 79.07 -101.33 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 SER A 399 OG 68.7 REMARK 620 3 YLA A 500 OAI 103.6 72.7 REMARK 620 4 HOH A2117 O 119.5 101.0 131.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YLA 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: 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: 4CH5 RELATED DB: PDB REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ADENYLATED REMARK 900 PROPIONYL LYSINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 21 AMINO ACIDS DISORDERED DBREF 4CH6 A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 4CH6 MET A 164 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 GLY A 165 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 SER A 166 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 SER A 167 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 168 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 169 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 170 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 171 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 172 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 173 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 SER A 174 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 SER A 175 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 GLY A 176 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 LEU A 177 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 VAL A 178 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 PRO A 179 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 ARG A 180 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 4CH6 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 YLA A 500 38 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 YLA (S)-2-AMINO-6-(((PROP-2-YN-1-YLOXY)CARBONYL)AMINO) HETNAM 2 YLA HEXANOIC (((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3, HETNAM 3 YLA 4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC) HETNAM 4 YLA ANHYDRIDE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 YLA C20 H28 N7 O10 P FORMUL 3 MG MG 2+ FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 HOH *117(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 GLU A 283 ILE A 288 5 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 HIS A 432 1 9 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 2.68 LINK OG SER A 399 MG MG A1455 1555 1555 2.80 LINK OAI YLA A 500 MG MG A1455 1555 1555 2.78 LINK MG MG A1455 O HOH A2117 1555 1555 2.43 CISPEP 1 ASP A 318 PRO A 319 0 -0.76 CISPEP 2 GLY A 403 PRO A 404 0 -0.38 SITE 1 AC1 23 ALA A 302 LEU A 305 TYR A 306 ARG A 330 SITE 2 AC1 23 GLU A 332 LEU A 339 PHE A 342 MET A 344 SITE 3 AC1 23 ASN A 346 GLU A 396 LEU A 397 SER A 398 SITE 4 AC1 23 SER A 399 TRP A 417 GLY A 419 ALA A 420 SITE 5 AC1 23 GLY A 421 GLY A 423 ARG A 426 MG A1455 SITE 6 AC1 23 HOH A2063 HOH A2074 HOH A2107 SITE 1 AC2 4 GLU A 396 SER A 399 YLA A 500 HOH A2117 SITE 1 AC3 5 TYR A 242 LEU A 246 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 A2065 SITE 1 AC5 6 ASN A 241 ARG A 439 ALA A 440 ASN A 448 SITE 2 AC5 6 GLY A 449 HOH A2111 SITE 1 AC6 4 TYR A 272 ASN A 307 ARG A 310 LYS A 311 SITE 1 AC7 6 ASP A 373 PHE A 374 LYS A 375 MET A 391 SITE 2 AC7 6 HIS A 392 GLY A 393 CRYST1 104.933 104.933 70.964 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 0.009530 0.005502 0.000000 0.00000 SCALE2 0.000000 0.011004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014092 0.00000