HEADER TRANSLATION 18-JUL-18 6AAP TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH ZAESECYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRROLYSINE--TRNA(PYL) LIGASE,PYRROLYSYL-TRNA SYNTHETASE, COMPND 5 PYLRS; COMPND 6 EC: 6.1.1.26; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI JCM 9314; SOURCE 3 ORGANISM_COMMON: METHANOSARCINA FRISIA; SOURCE 4 ORGANISM_TAXID: 1293038; SOURCE 5 GENE: PYLS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS AMINOACYL-TRNA SYNTHETASE, NON-NATURAL AMINO ACIDS, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR T.YANAGISAWA,M.KURATANI,S.YOKOYAMA REVDAT 4 22-NOV-23 6AAP 1 LINK REVDAT 3 07-AUG-19 6AAP 1 JRNL REVDAT 2 22-MAY-19 6AAP 1 SOURCE JRNL REVDAT 1 17-APR-19 6AAP 0 JRNL AUTH T.YANAGISAWA,M.KURATANI,E.SEKI,N.HINO,K.SAKAMOTO,S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR GENETIC-CODE EXPANSION WITH BULKY JRNL TITL 2 LYSINE DERIVATIVES BY AN ENGINEERED PYRROLYSYL-TRNA JRNL TITL 3 SYNTHETASE. JRNL REF CELL CHEM BIOL V. 26 936 2019 JRNL REFN ESSN 2451-9456 JRNL PMID 31031143 JRNL DOI 10.1016/J.CHEMBIOL.2019.03.008 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 43991 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2217 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 37.0519 - 3.7755 1.00 2735 134 0.1509 0.1858 REMARK 3 2 3.7755 - 2.9971 1.00 2659 139 0.1510 0.2057 REMARK 3 3 2.9971 - 2.6184 1.00 2620 146 0.1698 0.1926 REMARK 3 4 2.6184 - 2.3790 1.00 2619 164 0.1772 0.1806 REMARK 3 5 2.3790 - 2.2085 1.00 2594 153 0.1673 0.1910 REMARK 3 6 2.2085 - 2.0783 1.00 2657 110 0.1638 0.1874 REMARK 3 7 2.0783 - 1.9742 1.00 2618 124 0.1684 0.2025 REMARK 3 8 1.9742 - 1.8883 1.00 2586 141 0.1674 0.2071 REMARK 3 9 1.8883 - 1.8156 1.00 2620 146 0.1676 0.2146 REMARK 3 10 1.8156 - 1.7530 1.00 2591 141 0.1731 0.2081 REMARK 3 11 1.7530 - 1.6982 0.99 2592 145 0.1790 0.2177 REMARK 3 12 1.6982 - 1.6496 0.99 2591 128 0.1740 0.1893 REMARK 3 13 1.6496 - 1.6062 0.99 2602 122 0.1703 0.1992 REMARK 3 14 1.6062 - 1.5670 0.99 2566 139 0.1798 0.2036 REMARK 3 15 1.5670 - 1.5314 0.99 2580 133 0.1877 0.2254 REMARK 3 16 1.5314 - 1.4988 0.98 2544 152 0.1955 0.2309 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.005 2320 REMARK 3 ANGLE : 0.948 3139 REMARK 3 CHIRALITY : 0.079 338 REMARK 3 PLANARITY : 0.006 405 REMARK 3 DIHEDRAL : 17.613 918 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 188 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4997 28.7485 50.5386 REMARK 3 T TENSOR REMARK 3 T11: 0.1869 T22: 0.2935 REMARK 3 T33: 0.2201 T12: 0.0250 REMARK 3 T13: 0.0012 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.2342 L22: 3.9698 REMARK 3 L33: 2.8245 L12: -0.3949 REMARK 3 L13: -0.5066 L23: 1.3015 REMARK 3 S TENSOR REMARK 3 S11: -0.0558 S12: 0.1421 S13: -0.1512 REMARK 3 S21: -0.0772 S22: -0.0690 S23: 0.2716 REMARK 3 S31: 0.1855 S32: -0.3946 S33: 0.0988 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.7921 18.8361 43.5676 REMARK 3 T TENSOR REMARK 3 T11: 0.1766 T22: 0.1729 REMARK 3 T33: 0.1637 T12: -0.0051 REMARK 3 T13: 0.0142 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.5551 L22: 0.0646 REMARK 3 L33: 0.9775 L12: -0.0705 REMARK 3 L13: -0.5771 L23: -0.1069 REMARK 3 S TENSOR REMARK 3 S11: -0.1435 S12: -0.0667 S13: -0.0846 REMARK 3 S21: 0.1047 S22: 0.0095 S23: 0.0352 REMARK 3 S31: 0.1969 S32: -0.1384 S33: 0.1719 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 257 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.2354 34.4136 18.5015 REMARK 3 T TENSOR REMARK 3 T11: 0.1858 T22: 0.1221 REMARK 3 T33: 0.1671 T12: -0.0060 REMARK 3 T13: -0.0156 T23: 0.0327 REMARK 3 L TENSOR REMARK 3 L11: 1.5366 L22: 0.8219 REMARK 3 L33: 1.6293 L12: -0.1892 REMARK 3 L13: -0.3168 L23: 0.6536 REMARK 3 S TENSOR REMARK 3 S11: -0.0198 S12: 0.2012 S13: 0.2762 REMARK 3 S21: -0.1963 S22: -0.0126 S23: -0.0365 REMARK 3 S31: -0.3184 S32: -0.0778 S33: 0.0349 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.9462 25.9457 19.9917 REMARK 3 T TENSOR REMARK 3 T11: 0.1046 T22: 0.1412 REMARK 3 T33: 0.1459 T12: 0.0076 REMARK 3 T13: -0.0066 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 1.5026 L22: 1.4028 REMARK 3 L33: 1.5888 L12: 1.0946 REMARK 3 L13: 0.4793 L23: 0.3084 REMARK 3 S TENSOR REMARK 3 S11: -0.0748 S12: 0.0662 S13: 0.0805 REMARK 3 S21: -0.0063 S22: -0.0107 S23: 0.1163 REMARK 3 S31: 0.0598 S32: -0.1992 S33: 0.1067 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 371 THROUGH 454 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9412 28.5667 23.5385 REMARK 3 T TENSOR REMARK 3 T11: 0.1317 T22: 0.1467 REMARK 3 T33: 0.1670 T12: 0.0101 REMARK 3 T13: -0.0060 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.0844 L22: 0.4860 REMARK 3 L33: 1.4594 L12: 0.1610 REMARK 3 L13: -0.0665 L23: 0.0360 REMARK 3 S TENSOR REMARK 3 S11: -0.0713 S12: 0.0784 S13: 0.1265 REMARK 3 S21: -0.0404 S22: 0.0248 S23: 0.0592 REMARK 3 S31: -0.0779 S32: -0.2353 S33: 0.0072 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 6AAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-14 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 : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43994 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 29.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 85.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: 2ZIM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL (PH 8.5), PEG 200, KCL, REMARK 280 MGCL2, SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.39850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.80450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.39850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.80450 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: 6850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 64.92012 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 62.97547 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 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 ASP A 281 CG OD1 OD2 REMARK 470 GLU A 283 CG CD OE1 OE2 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 O HOH A 692 O HOH A 799 2.10 REMARK 500 O HOH A 731 O HOH A 764 2.13 REMARK 500 NH2 ARG A 356 O HOH A 601 2.14 REMARK 500 O HOH A 611 O HOH A 812 2.17 REMARK 500 O HOH A 626 O HOH A 857 2.18 REMARK 500 O HOH A 607 O HOH A 800 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 GLU A 207 62.04 -104.90 REMARK 500 GLU A 238 -67.26 -127.68 REMARK 500 ASP A 292 -124.92 57.48 REMARK 500 ASP A 334 88.82 62.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 873 DISTANCE = 6.60 ANGSTROMS 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 A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 207 OE2 REMARK 620 2 GLU A 396 OE1 76.2 REMARK 620 3 ATP A 504 O1G 71.0 5.1 REMARK 620 4 ATP A 504 O1B 74.7 3.2 4.6 REMARK 620 5 HOH A 637 O 77.9 1.8 6.9 4.7 REMARK 620 6 HOH A 716 O 74.5 4.6 5.4 7.0 5.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE2 REMARK 620 2 SER A 399 OG 89.7 REMARK 620 3 ATP A 504 O1B 90.5 172.7 REMARK 620 4 ATP A 504 O1A 94.5 95.0 92.3 REMARK 620 5 HOH A 637 O 87.2 89.3 83.4 175.4 REMARK 620 6 HOH A 732 O 173.4 90.4 88.6 92.1 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 504 O2G REMARK 620 2 ATP A 504 O2B 89.2 REMARK 620 3 HOH A 640 O 94.1 91.4 REMARK 620 4 HOH A 682 O 176.5 87.4 85.1 REMARK 620 5 HOH A 691 O 94.5 176.2 88.1 88.9 REMARK 620 6 HOH A 750 O 90.5 90.5 175.0 90.4 89.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9U6 A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6AAC RELATED DB: PDB REMARK 900 RELATED ID: 6AAD RELATED DB: PDB REMARK 900 RELATED ID: 6AAN RELATED DB: PDB REMARK 900 RELATED ID: 6AAO RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE REFERENCE Q8PWY1 (PYLS_METMA) IS DERIVED FROM A REMARK 999 DIFFERENT STRAIN (METHANOSARCINA MAZEI GO1, TAXID 192952). RESIDUE REMARK 999 E444G IS A NATURAL MUTATION OBSERVED IN PYLRS GENE FROM REMARK 999 METHANOSARCINA MAZEI JCM 9314 GENOME. DBREF 6AAP A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 6AAP GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAP SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAP HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAP MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAP ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 6AAP PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 6AAP GLY A 444 UNP Q8PWY1 GLU 444 SEE SEQUENCE DETAILS SEQRES 1 A 274 GLY SER HIS MET ALA SER ALA PRO ALA LEU THR LYS SER SEQRES 2 A 274 GLN THR ASP ARG LEU GLU VAL LEU LEU ASN PRO LYS ASP SEQRES 3 A 274 GLU ILE SER LEU ASN SER GLY LYS PRO PHE ARG GLU LEU SEQRES 4 A 274 GLU SER GLU LEU LEU SER ARG ARG LYS LYS ASP LEU GLN SEQRES 5 A 274 GLN ILE TYR ALA GLU GLU ARG GLU ASN TYR LEU GLY LYS SEQRES 6 A 274 LEU GLU ARG GLU ILE THR ARG PHE PHE VAL ASP ARG GLY SEQRES 7 A 274 PHE LEU GLU ILE LYS SER PRO ILE LEU ILE PRO LEU GLU SEQRES 8 A 274 TYR ILE GLU ARG MET GLY ILE ASP ASN ASP THR GLU LEU SEQRES 9 A 274 SER LYS GLN ILE PHE ARG VAL ASP LYS ASN PHE CYS LEU SEQRES 10 A 274 ARG PRO MET LEU ALA PRO ASN LEU ALA ASN TYR LEU ARG SEQRES 11 A 274 LYS LEU ASP ARG ALA LEU PRO ASP PRO ILE LYS ILE PHE SEQRES 12 A 274 GLU ILE GLY PRO CYS TYR ARG LYS GLU SER ASP GLY LYS SEQRES 13 A 274 GLU HIS LEU GLU GLU PHE THR MET LEU ASN PHE CYS GLN SEQRES 14 A 274 MET GLY SER GLY CYS THR ARG GLU ASN LEU GLU SER ILE SEQRES 15 A 274 ILE THR ASP PHE LEU ASN HIS LEU GLY ILE ASP PHE LYS SEQRES 16 A 274 ILE VAL GLY ASP SER CYS MET VAL PHE GLY ASP THR LEU SEQRES 17 A 274 ASP VAL MET HIS GLY ASP LEU GLU LEU SER SER ALA VAL SEQRES 18 A 274 VAL GLY PRO ILE PRO LEU ASP ARG GLU TRP GLY ILE ASP SEQRES 19 A 274 LYS PRO TRP ILE GLY ALA GLY PHE GLY LEU GLU ARG LEU SEQRES 20 A 274 LEU LYS VAL LYS HIS ASP PHE LYS ASN ILE LYS ARG ALA SEQRES 21 A 274 ALA ARG SER GLY SER TYR TYR ASN GLY ILE SER THR ASN SEQRES 22 A 274 LEU HET MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET ATP A 504 31 HET 9U6 A 505 40 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 9U6 3-[(2-{[(BENZYLOXY)CARBONYL]AMINO}ETHYL)SELANYL]-L- HETNAM 2 9U6 ALANINE FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 9U6 C13 H18 N2 O4 SE FORMUL 7 HOH *273(H2 O) HELIX 1 AA1 THR A 191 LEU A 202 1 12 HELIX 2 AA2 PRO A 215 GLU A 238 1 24 HELIX 3 AA3 ASN A 241 ARG A 257 1 17 HELIX 4 AA4 LEU A 270 MET A 276 1 7 HELIX 5 AA5 THR A 282 GLN A 287 1 6 HELIX 6 AA6 LEU A 301 ASP A 313 1 13 HELIX 7 AA7 THR A 355 GLY A 371 1 17 HELIX 8 AA8 ILE A 405 GLY A 412 5 8 HELIX 9 AA9 LEU A 424 ASP A 433 1 10 HELIX 10 AB1 ASN A 436 ALA A 441 5 6 SHEET 1 AA1 7 LEU A 260 ILE A 262 0 SHEET 2 AA1 7 ILE A 320 TYR A 329 1 O PHE A 323 N ILE A 262 SHEET 3 AA1 7 GLU A 341 MET A 350 -1 O MET A 344 N GLY A 326 SHEET 4 AA1 7 TRP A 417 GLY A 423 -1 O PHE A 422 N LEU A 345 SHEET 5 AA1 7 LEU A 395 VAL A 402 -1 N VAL A 401 O GLY A 419 SHEET 6 AA1 7 GLY A 385 HIS A 392 -1 N VAL A 390 O LEU A 397 SHEET 7 AA1 7 LYS A 375 CYS A 381 -1 N VAL A 377 O ASP A 389 SHEET 1 AA2 3 LEU A 267 PRO A 269 0 SHEET 2 AA2 3 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 3 AA2 3 ARG A 290 VAL A 291 -1 N VAL A 291 O PHE A 295 SHEET 1 AA3 2 TYR A 446 TYR A 447 0 SHEET 2 AA3 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447 LINK OE2 GLU A 207 MG MG A 503 1555 4546 2.00 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.11 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.11 LINK OG SER A 399 MG MG A 502 1555 1555 2.06 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.06 LINK MG MG A 501 O2B ATP A 504 1555 1555 2.01 LINK MG MG A 501 O HOH A 640 1555 1555 2.05 LINK MG MG A 501 O HOH A 682 1555 1555 2.19 LINK MG MG A 501 O HOH A 691 1555 1555 2.07 LINK MG MG A 501 O HOH A 750 1555 1555 2.12 LINK MG MG A 502 O1B ATP A 504 1555 1555 2.07 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.03 LINK MG MG A 502 O HOH A 637 1555 1555 2.17 LINK MG MG A 502 O HOH A 732 1555 1555 2.07 LINK MG MG A 503 O1G ATP A 504 1555 1555 2.09 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.24 LINK MG MG A 503 O HOH A 637 1555 1555 2.23 LINK MG MG A 503 O HOH A 716 1555 4556 2.09 CISPEP 1 ASP A 318 PRO A 319 0 -1.21 CISPEP 2 GLY A 403 PRO A 404 0 -2.03 SITE 1 AC1 5 ATP A 504 HOH A 640 HOH A 682 HOH A 691 SITE 2 AC1 5 HOH A 750 SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 6 HOH A 637 HOH A 732 SITE 1 AC3 6 GLU A 207 GLU A 396 MG A 502 ATP A 504 SITE 2 AC3 6 HOH A 637 HOH A 716 SITE 1 AC4 31 GLU A 207 ARG A 330 GLU A 332 HIS A 338 SITE 2 AC4 31 LEU A 339 PHE A 342 MET A 344 GLU A 396 SITE 3 AC4 31 LEU A 397 SER A 398 SER A 399 GLY A 421 SITE 4 AC4 31 GLY A 423 ARG A 426 MG A 501 MG A 502 SITE 5 AC4 31 MG A 503 9U6 A 505 HOH A 611 HOH A 637 SITE 6 AC4 31 HOH A 640 HOH A 682 HOH A 691 HOH A 716 SITE 7 AC4 31 HOH A 731 HOH A 732 HOH A 745 HOH A 748 SITE 8 AC4 31 HOH A 750 HOH A 764 HOH A 768 SITE 1 AC5 17 MET A 276 MET A 300 ALA A 302 ALA A 306 SITE 2 AC5 17 LEU A 309 ARG A 330 ASN A 346 CYS A 348 SITE 3 AC5 17 PHE A 384 SER A 399 ASP A 408 ILE A 413 SITE 4 AC5 17 TRP A 417 GLY A 421 ATP A 504 HOH A 603 SITE 5 AC5 17 HOH A 787 CRYST1 100.797 43.609 72.478 90.00 119.67 90.00 C 1 2 1 4 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 0.009921 0.000000 0.005651 0.00000 SCALE2 0.000000 0.022931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015879 0.00000