HEADER TRANSLATION 22-JUL-18 6ABM TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH PTMDZLYS 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, PYRROLYSYL-TRNA KEYWDS 2 SYNTHETASE, TRNA, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR T.YANAGISAWA,M.KURATANI,S.YOKOYAMA REVDAT 4 22-NOV-23 6ABM 1 LINK REVDAT 3 07-AUG-19 6ABM 1 JRNL REVDAT 2 22-MAY-19 6ABM 1 SOURCE JRNL REVDAT 1 17-APR-19 6ABM 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. 1.37 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 59367 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.370 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 35.0353 - 3.2959 0.99 4237 148 0.1395 0.1753 REMARK 3 2 3.2959 - 2.6163 1.00 4189 146 0.1588 0.1816 REMARK 3 3 2.6163 - 2.2856 1.00 4155 145 0.1718 0.2021 REMARK 3 4 2.2856 - 2.0767 1.00 4154 144 0.1593 0.2253 REMARK 3 5 2.0767 - 1.9279 1.00 4120 144 0.1714 0.2151 REMARK 3 6 1.9279 - 1.8142 1.00 4143 145 0.1767 0.2184 REMARK 3 7 1.8142 - 1.7233 1.00 4116 143 0.1828 0.2470 REMARK 3 8 1.7233 - 1.6483 1.00 4127 144 0.1730 0.2034 REMARK 3 9 1.6483 - 1.5849 1.00 4097 143 0.1734 0.1848 REMARK 3 10 1.5849 - 1.5302 1.00 4143 145 0.1718 0.2166 REMARK 3 11 1.5302 - 1.4823 1.00 4096 141 0.1832 0.2284 REMARK 3 12 1.4823 - 1.4400 0.99 4096 143 0.2010 0.2291 REMARK 3 13 1.4400 - 1.4021 0.99 4098 144 0.2152 0.2110 REMARK 3 14 1.4021 - 1.3678 0.88 3596 125 0.2380 0.2770 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.850 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 : 0.008 2359 REMARK 3 ANGLE : 1.112 3207 REMARK 3 CHIRALITY : 0.088 345 REMARK 3 PLANARITY : 0.007 414 REMARK 3 DIHEDRAL : 17.459 942 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 188 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7636 22.4675 12.4769 REMARK 3 T TENSOR REMARK 3 T11: 0.1789 T22: 0.2938 REMARK 3 T33: 0.1988 T12: -0.0231 REMARK 3 T13: 0.0187 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.0703 L22: 2.7891 REMARK 3 L33: 2.4044 L12: 0.4748 REMARK 3 L13: -0.0323 L23: -0.3050 REMARK 3 S TENSOR REMARK 3 S11: -0.0671 S12: -0.1723 S13: -0.1293 REMARK 3 S21: -0.0282 S22: -0.0884 S23: -0.1784 REMARK 3 S31: 0.2762 S32: 0.4066 S33: 0.1279 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6342 12.0391 19.4835 REMARK 3 T TENSOR REMARK 3 T11: 0.1737 T22: 0.1566 REMARK 3 T33: 0.1722 T12: 0.0033 REMARK 3 T13: 0.0298 T23: -0.0227 REMARK 3 L TENSOR REMARK 3 L11: 0.8153 L22: 0.3612 REMARK 3 L33: 1.0913 L12: 0.4002 REMARK 3 L13: -0.4626 L23: -0.1947 REMARK 3 S TENSOR REMARK 3 S11: -0.1787 S12: 0.1467 S13: -0.1662 REMARK 3 S21: -0.1456 S22: 0.0376 S23: -0.0941 REMARK 3 S31: 0.1753 S32: 0.0542 S33: 0.1844 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 257 THROUGH 284 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.8920 29.5372 44.8547 REMARK 3 T TENSOR REMARK 3 T11: 0.2485 T22: 0.1690 REMARK 3 T33: 0.2009 T12: 0.0096 REMARK 3 T13: -0.0088 T23: -0.0453 REMARK 3 L TENSOR REMARK 3 L11: 1.5225 L22: 1.3655 REMARK 3 L33: 1.5739 L12: -0.2772 REMARK 3 L13: -0.5130 L23: -0.2991 REMARK 3 S TENSOR REMARK 3 S11: 0.0229 S12: -0.1977 S13: 0.3302 REMARK 3 S21: 0.1811 S22: 0.0379 S23: -0.1352 REMARK 3 S31: -0.4100 S32: 0.0812 S33: 0.0600 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 285 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7133 26.7541 44.6897 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.1386 REMARK 3 T33: 0.1326 T12: 0.0176 REMARK 3 T13: -0.0176 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 1.7450 L22: 1.0326 REMARK 3 L33: 1.7268 L12: 0.2504 REMARK 3 L13: -0.4883 L23: -0.2158 REMARK 3 S TENSOR REMARK 3 S11: 0.0019 S12: -0.2171 S13: 0.1959 REMARK 3 S21: 0.1462 S22: 0.0241 S23: 0.0450 REMARK 3 S31: -0.2850 S32: 0.0807 S33: 0.0146 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6929 19.0554 43.1438 REMARK 3 T TENSOR REMARK 3 T11: 0.1038 T22: 0.1531 REMARK 3 T33: 0.1402 T12: -0.0023 REMARK 3 T13: -0.0268 T23: -0.0160 REMARK 3 L TENSOR REMARK 3 L11: 1.4927 L22: 1.4638 REMARK 3 L33: 1.5840 L12: -0.8999 REMARK 3 L13: 0.0343 L23: -0.2457 REMARK 3 S TENSOR REMARK 3 S11: -0.0897 S12: -0.1277 S13: 0.0779 REMARK 3 S21: 0.0377 S22: 0.0238 S23: -0.1491 REMARK 3 S31: 0.0048 S32: 0.1959 S33: 0.0958 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 371 THROUGH 384 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5518 21.6744 46.6344 REMARK 3 T TENSOR REMARK 3 T11: 0.2693 T22: 0.2966 REMARK 3 T33: 0.2483 T12: 0.0130 REMARK 3 T13: -0.0244 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 1.7760 L22: 4.7747 REMARK 3 L33: 2.6244 L12: 0.2253 REMARK 3 L13: -0.6265 L23: 2.8173 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: -0.2715 S13: 0.3794 REMARK 3 S21: -0.1309 S22: 0.0658 S23: -0.2116 REMARK 3 S31: -0.4251 S32: 0.2229 S33: -0.2507 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 385 THROUGH 454 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.3370 21.5346 37.9497 REMARK 3 T TENSOR REMARK 3 T11: 0.1211 T22: 0.1389 REMARK 3 T33: 0.1506 T12: -0.0029 REMARK 3 T13: -0.0067 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.9698 L22: 0.4883 REMARK 3 L33: 1.8340 L12: -0.1007 REMARK 3 L13: -0.2787 L23: -0.0995 REMARK 3 S TENSOR REMARK 3 S11: -0.0820 S12: -0.0627 S13: 0.0489 REMARK 3 S21: 0.0383 S22: 0.0485 S23: -0.0725 REMARK 3 S31: -0.0803 S32: 0.1818 S33: -0.0717 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 6ABM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-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 : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59383 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.368 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 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 <I/SIGMA(I)> 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, 2ZCE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL BUFFER (PH 8.5), PEG 200, REMARK 280 KCL, 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 50.80200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.10450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.80200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.10450 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: 8520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 -34.59704 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.77290 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 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 721 O HOH A 824 2.10 REMARK 500 O HOH A 608 O HOH A 655 2.15 REMARK 500 O HOH A 613 O HOH A 834 2.15 REMARK 500 O HOH A 610 O HOH A 834 2.17 REMARK 500 O HOH A 603 O HOH A 766 2.17 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 238 -63.09 -123.86 REMARK 500 ASN A 280 7.37 -65.33 REMARK 500 ASP A 292 -136.28 62.28 REMARK 500 ASN A 453 77.24 -100.32 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 926 DISTANCE = 7.17 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 K A 506 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 204 O REMARK 620 2 ASP A 206 O 77.0 REMARK 620 3 HOH A 714 O 84.9 66.1 REMARK 620 4 HOH A 863 O 88.3 82.9 149.1 REMARK 620 5 HOH A 866 O 163.3 86.4 87.2 91.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 508 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 368 OD1 REMARK 620 2 ILE A 372 O 139.8 REMARK 620 3 HOH A 623 O 100.6 119.3 REMARK 620 4 HOH A 828 O 100.4 95.2 73.5 REMARK 620 N 1 2 3 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 91.4 REMARK 620 3 ATP A 504 O2A 96.7 95.2 REMARK 620 4 ATP A 504 O2B 90.9 172.4 91.8 REMARK 620 5 HOH A 648 O 90.9 86.9 172.1 85.9 REMARK 620 6 HOH A 772 O 175.8 88.4 87.6 88.7 84.9 REMARK 620 N 1 2 3 4 5 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 396 OE1 REMARK 620 2 ATP A 504 O2B 93.3 REMARK 620 3 ATP A 504 O3G 92.4 86.1 REMARK 620 4 HOH A 648 O 78.3 79.0 161.8 REMARK 620 5 HOH A 803 O 85.1 173.9 99.8 95.0 REMARK 620 6 HOH A 815 O 171.5 85.9 96.0 93.3 94.8 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 O1B 90.3 REMARK 620 3 HOH A 645 O 93.4 92.6 REMARK 620 4 HOH A 669 O 91.4 177.6 85.6 REMARK 620 5 HOH A 744 O 178.3 88.0 86.1 90.2 REMARK 620 6 HOH A 778 O 88.5 93.2 173.8 88.5 92.1 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 9VR A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 508 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 900 RELATED ID: 6AAP RELATED DB: PDB REMARK 900 RELATED ID: 6AAQ RELATED DB: PDB REMARK 900 RELATED ID: 6AAZ RELATED DB: PDB REMARK 900 RELATED ID: 6AB0 RELATED DB: PDB REMARK 900 RELATED ID: 6AB1 RELATED DB: PDB REMARK 900 RELATED ID: 6AB2 RELATED DB: PDB REMARK 900 RELATED ID: 6AB8 RELATED DB: PDB REMARK 900 RELATED ID: 6ABK RELATED DB: PDB REMARK 900 RELATED ID: 6ABL 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 6ABM A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 6ABM GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABM SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABM HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABM MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABM ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 6ABM PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 6ABM 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 9VR A 505 27 HET K A 506 1 HET K A 508 1 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 9VR (2S)-2-AZANYL-6-[[4-[3-(TRIFLUOROMETHYL)-1,2-DIAZIRIN- HETNAM 2 9VR 3-YL]PHENYL]METHOXYCARBONYLAMINO]HEXANOIC ACID HETNAM K POTASSIUM ION FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 9VR C16 H19 F3 N4 O4 FORMUL 7 K 2(K 1+) FORMUL 9 HOH *326(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 LEU A 284 ILE A 288 5 5 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 O PRO A 204 K K A 506 1555 1555 2.66 LINK O ASP A 206 K K A 506 1555 1555 2.74 LINK OD1 ASN A 368 K K A 508 1555 1555 2.76 LINK O ILE A 372 K K A 508 1555 1555 2.61 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.16 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.31 LINK OG SER A 399 MG MG A 502 1555 1555 2.08 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.07 LINK MG MG A 501 O1B ATP A 504 1555 1555 2.03 LINK MG MG A 501 O HOH A 645 1555 1555 2.14 LINK MG MG A 501 O HOH A 669 1555 1555 2.12 LINK MG MG A 501 O HOH A 744 1555 1555 2.08 LINK MG MG A 501 O HOH A 778 1555 1555 2.13 LINK MG MG A 502 O2A ATP A 504 1555 1555 2.11 LINK MG MG A 502 O2B ATP A 504 1555 1555 2.12 LINK MG MG A 502 O HOH A 648 1555 1555 2.21 LINK MG MG A 502 O HOH A 772 1555 1555 2.12 LINK MG MG A 503 O2B ATP A 504 1555 1555 2.30 LINK MG MG A 503 O3G ATP A 504 1555 1555 2.19 LINK MG MG A 503 O HOH A 648 1555 1555 2.33 LINK MG MG A 503 O HOH A 803 1555 1555 2.13 LINK MG MG A 503 O HOH A 815 1555 1555 2.18 LINK K K A 506 O HOH A 714 1555 1555 2.56 LINK K K A 506 O HOH A 863 1555 1555 2.89 LINK K K A 506 O HOH A 866 1555 1555 2.74 LINK K K A 508 O HOH A 623 1555 1555 2.81 LINK K K A 508 O HOH A 828 1555 1555 2.94 CISPEP 1 ASP A 318 PRO A 319 0 -3.31 CISPEP 2 GLY A 403 PRO A 404 0 -1.57 SITE 1 AC1 5 ATP A 504 HOH A 645 HOH A 669 HOH A 744 SITE 2 AC1 5 HOH A 778 SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 6 HOH A 648 HOH A 772 SITE 1 AC3 6 GLU A 396 MG A 502 ATP A 504 HOH A 648 SITE 2 AC3 6 HOH A 803 HOH A 815 SITE 1 AC4 27 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC4 27 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC4 27 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC4 27 ARG A 426 MG A 501 MG A 502 MG A 503 SITE 5 AC4 27 9VR A 505 HOH A 645 HOH A 648 HOH A 669 SITE 6 AC4 27 HOH A 705 HOH A 707 HOH A 744 HOH A 745 SITE 7 AC4 27 HOH A 772 HOH A 778 HOH A 815 SITE 1 AC5 15 MET A 276 ALA A 302 ALA A 306 ASN A 346 SITE 2 AC5 15 CYS A 348 PHE A 384 SER A 399 LEU A 407 SITE 3 AC5 15 ASP A 408 TRP A 411 TRP A 417 GLY A 419 SITE 4 AC5 15 ALA A 420 ATP A 504 HOH A 817 SITE 1 AC6 5 PRO A 204 ASP A 206 HOH A 714 HOH A 863 SITE 2 AC6 5 HOH A 866 SITE 1 AC7 3 GLU A 341 ARG A 442 HOH A 721 SITE 1 AC8 4 ASN A 368 ILE A 372 HOH A 623 HOH A 828 CRYST1 101.604 44.209 72.553 90.00 118.48 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 0.009842 0.000000 0.005340 0.00000 SCALE2 0.000000 0.022620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015681 0.00000