HEADER TRANSLATION 19-JUL-18 6AB2 TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH OCLZLYS 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 6AB2 1 LINK REVDAT 3 07-AUG-19 6AB2 1 JRNL REVDAT 2 22-MAY-19 6AB2 1 SOURCE JRNL REVDAT 1 17-APR-19 6AB2 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 53394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.750 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 35.0817 - 3.3735 0.97 3788 148 0.1551 0.1696 REMARK 3 2 3.3735 - 2.6780 0.99 3789 147 0.1708 0.2370 REMARK 3 3 2.6780 - 2.3395 0.99 3753 146 0.1827 0.1881 REMARK 3 4 2.3395 - 2.1257 0.99 3696 143 0.1670 0.2027 REMARK 3 5 2.1257 - 1.9733 0.98 3709 145 0.1700 0.2039 REMARK 3 6 1.9733 - 1.8570 0.98 3700 144 0.1730 0.1918 REMARK 3 7 1.8570 - 1.7640 0.98 3654 142 0.1816 0.2035 REMARK 3 8 1.7640 - 1.6872 0.97 3652 142 0.1789 0.2200 REMARK 3 9 1.6872 - 1.6222 0.97 3653 143 0.1726 0.1875 REMARK 3 10 1.6222 - 1.5663 0.97 3639 141 0.1760 0.2012 REMARK 3 11 1.5663 - 1.5173 0.97 3613 140 0.1762 0.2118 REMARK 3 12 1.5173 - 1.4739 0.96 3614 141 0.1882 0.1890 REMARK 3 13 1.4739 - 1.4351 0.96 3615 141 0.1927 0.2334 REMARK 3 14 1.4351 - 1.4001 0.95 3519 137 0.2182 0.2490 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.540 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 : 0.006 2335 REMARK 3 ANGLE : 1.047 3155 REMARK 3 CHIRALITY : 0.082 337 REMARK 3 PLANARITY : 0.007 406 REMARK 3 DIHEDRAL : 17.847 933 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 188 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.9276 28.4356 50.4977 REMARK 3 T TENSOR REMARK 3 T11: 0.1542 T22: 0.2766 REMARK 3 T33: 0.2417 T12: 0.0268 REMARK 3 T13: 0.0173 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 2.8839 L22: 3.5647 REMARK 3 L33: 3.3691 L12: -0.5080 REMARK 3 L13: -1.6107 L23: 0.8786 REMARK 3 S TENSOR REMARK 3 S11: -0.1295 S12: 0.2317 S13: -0.2339 REMARK 3 S21: -0.0687 S22: -0.0638 S23: 0.3721 REMARK 3 S31: 0.2934 S32: -0.3353 S33: 0.1277 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2163 18.5764 43.7441 REMARK 3 T TENSOR REMARK 3 T11: 0.1808 T22: 0.1595 REMARK 3 T33: 0.1870 T12: 0.0057 REMARK 3 T13: 0.0473 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 0.4826 L22: 0.0966 REMARK 3 L33: 0.4881 L12: -0.1496 REMARK 3 L13: -0.3042 L23: -0.0324 REMARK 3 S TENSOR REMARK 3 S11: -0.1680 S12: -0.0957 S13: -0.1145 REMARK 3 S21: 0.1107 S22: 0.0493 S23: 0.0464 REMARK 3 S31: 0.2009 S32: -0.0831 S33: 0.2399 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 257 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9676 33.7525 18.6214 REMARK 3 T TENSOR REMARK 3 T11: 0.1709 T22: 0.1172 REMARK 3 T33: 0.1813 T12: -0.0146 REMARK 3 T13: 0.0024 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 1.4428 L22: 1.0912 REMARK 3 L33: 1.5601 L12: -0.2295 REMARK 3 L13: -0.2224 L23: 0.4767 REMARK 3 S TENSOR REMARK 3 S11: -0.0533 S12: 0.1985 S13: 0.2613 REMARK 3 S21: -0.1509 S22: 0.0161 S23: -0.0369 REMARK 3 S31: -0.3026 S32: -0.0872 S33: 0.0436 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.2414 25.5796 19.8394 REMARK 3 T TENSOR REMARK 3 T11: 0.1081 T22: 0.1476 REMARK 3 T33: 0.1771 T12: -0.0058 REMARK 3 T13: 0.0113 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.1338 L22: 1.1111 REMARK 3 L33: 1.7578 L12: 0.8083 REMARK 3 L13: 0.4598 L23: 0.4167 REMARK 3 S TENSOR REMARK 3 S11: -0.0702 S12: 0.0612 S13: 0.0719 REMARK 3 S21: -0.0194 S22: -0.0165 S23: 0.1024 REMARK 3 S31: 0.0335 S32: -0.2473 S33: 0.0474 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 371 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9141 28.1717 17.4750 REMARK 3 T TENSOR REMARK 3 T11: 0.1711 T22: 0.2440 REMARK 3 T33: 0.2473 T12: -0.0125 REMARK 3 T13: -0.0069 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 3.0310 L22: 0.9839 REMARK 3 L33: 4.6418 L12: 0.2487 REMARK 3 L13: -1.4589 L23: -1.0212 REMARK 3 S TENSOR REMARK 3 S11: -0.0125 S12: 0.2122 S13: 0.4834 REMARK 3 S21: -0.1272 S22: 0.1997 S23: 0.3274 REMARK 3 S31: -0.3495 S32: -0.4727 S33: -0.0979 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 403 THROUGH 454 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3240 28.3630 27.0939 REMARK 3 T TENSOR REMARK 3 T11: 0.0834 T22: 0.1068 REMARK 3 T33: 0.1693 T12: 0.0097 REMARK 3 T13: 0.0018 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.0564 L22: 0.7037 REMARK 3 L33: 2.6542 L12: 0.1493 REMARK 3 L13: -0.2492 L23: -0.2291 REMARK 3 S TENSOR REMARK 3 S11: -0.1225 S12: 0.0201 S13: 0.0840 REMARK 3 S21: 0.0037 S22: 0.0244 S23: 0.0615 REMARK 3 S31: -0.0226 S32: -0.2211 S33: -0.0117 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 6AB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-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) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53399 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 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 (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 50.70950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.94350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.70950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.94350 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: 8850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 65.82942 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.03265 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 465 ASP A 281 REMARK 465 THR A 282 REMARK 465 GLU A 283 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 601 O HOH A 629 2.09 REMARK 500 NZ LYS A 286 O HOH A 601 2.10 REMARK 500 O HOH A 633 O HOH A 760 2.12 REMARK 500 O ILE A 208 O HOH A 602 2.12 REMARK 500 O HOH A 794 O HOH A 846 2.13 REMARK 500 O HOH A 674 O HOH A 751 2.17 REMARK 500 NH1 ARG A 257 O HOH A 603 2.17 REMARK 500 O HOH A 801 O HOH A 804 2.17 REMARK 500 OE2 GLU A 199 O HOH A 604 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 808 O HOH A 846 4556 2.11 REMARK 500 O HOH A 727 O HOH A 846 1565 2.13 REMARK 500 O HOH A 825 O HOH A 842 4546 2.16 REMARK 500 O HOH A 721 O HOH A 843 4546 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 65.97 -103.05 REMARK 500 GLU A 237 -86.75 -110.47 REMARK 500 ASP A 292 -140.67 58.81 REMARK 500 ASP A 334 -70.87 -116.28 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 875 DISTANCE = 6.89 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 507 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 203 O REMARK 620 2 ASP A 206 O 82.8 REMARK 620 3 HOH A 602 O 128.3 67.4 REMARK 620 4 HOH A 619 O 102.8 56.3 94.6 REMARK 620 5 HOH A 836 O 79.8 152.2 140.1 107.0 REMARK 620 N 1 2 3 4 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 71.0 REMARK 620 3 ATP A 504 O1G 65.9 5.4 REMARK 620 4 ATP A 504 O1B 67.9 3.8 4.4 REMARK 620 5 HOH A 611 O 70.5 4.3 5.2 7.0 REMARK 620 6 HOH A 693 O 72.2 1.2 6.5 4.8 4.7 REMARK 620 N 1 2 3 4 5 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 GLU A 341 OE1 REMARK 620 2 ARG A 442 O 113.7 REMARK 620 3 EDO A 510 O1 121.8 124.4 REMARK 620 N 1 2 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 84.1 REMARK 620 3 ATP A 504 O1A 100.2 94.8 REMARK 620 4 ATP A 504 O1B 91.0 173.2 90.7 REMARK 620 5 HOH A 693 O 87.1 89.4 171.9 85.5 REMARK 620 6 HOH A 722 O 172.9 91.7 85.9 92.6 87.1 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 94.1 REMARK 620 3 HOH A 647 O 92.8 92.3 REMARK 620 4 HOH A 649 O 92.8 172.8 89.7 REMARK 620 5 HOH A 690 O 88.9 88.6 178.0 89.2 REMARK 620 6 HOH A 747 O 169.6 92.4 78.8 81.2 99.4 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 9V6 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9V6 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 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511 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 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 6AB2 A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 6AB2 GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AB2 SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AB2 HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AB2 MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AB2 ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 6AB2 PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 6AB2 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 9V6 A 505 21 HET 9V6 A 506 21 HET K A 507 1 HET K A 508 1 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 9V6 (2S)-2-AZANYL-6-[(2-CHLOROPHENYL) HETNAM 2 9V6 METHOXYCARBONYLAMINO]HEXANOIC ACID HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 9V6 2(C14 H19 CL N2 O4) FORMUL 8 K 2(K 1+) FORMUL 10 EDO 3(C2 H6 O2) FORMUL 13 HOH *275(H2 O) HELIX 1 AA1 THR A 191 LEU A 202 1 12 HELIX 2 AA2 PRO A 215 GLU A 237 1 23 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 350 N ILE A 320 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 ASN A 203 K K A 507 1555 1555 3.04 LINK O ASP A 206 K K A 507 1555 1555 3.20 LINK OE2 GLU A 207 MG MG A 503 1555 4546 2.29 LINK OE1 GLU A 341 K K A 508 1555 1555 2.66 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.34 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.26 LINK OG SER A 399 MG MG A 502 1555 1555 2.09 LINK O ARG A 442 K K A 508 1555 1555 2.63 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.12 LINK MG MG A 501 O2B ATP A 504 1555 1555 1.88 LINK MG MG A 501 O HOH A 647 1555 1555 1.97 LINK MG MG A 501 O HOH A 649 1555 1555 2.16 LINK MG MG A 501 O HOH A 690 1555 1555 2.06 LINK MG MG A 501 O HOH A 747 1555 1555 2.45 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.04 LINK MG MG A 502 O1B ATP A 504 1555 1555 2.00 LINK MG MG A 502 O HOH A 693 1555 1555 2.25 LINK MG MG A 502 O HOH A 722 1555 1555 2.10 LINK MG MG A 503 O1G ATP A 504 1555 1555 2.03 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.22 LINK MG MG A 503 O HOH A 611 1555 4556 2.11 LINK MG MG A 503 O HOH A 693 1555 1555 2.14 LINK K K A 507 O HOH A 602 1555 1555 2.78 LINK K K A 507 O HOH A 619 1555 1555 2.75 LINK K K A 507 O HOH A 836 1555 1555 2.99 LINK K K A 508 O1 EDO A 510 1555 1555 2.67 CISPEP 1 ASP A 318 PRO A 319 0 -0.78 CISPEP 2 SER A 333 ASP A 334 0 6.91 CISPEP 3 GLY A 403 PRO A 404 0 -3.82 SITE 1 AC1 5 ATP A 504 HOH A 647 HOH A 649 HOH A 690 SITE 2 AC1 5 HOH A 747 SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 6 HOH A 693 HOH A 722 SITE 1 AC3 6 GLU A 207 GLU A 396 MG A 502 ATP A 504 SITE 2 AC3 6 HOH A 611 HOH A 693 SITE 1 AC4 26 GLU A 207 ARG A 330 GLU A 332 HIS A 338 SITE 2 AC4 26 LEU A 339 PHE A 342 MET A 344 GLU A 396 SITE 3 AC4 26 LEU A 397 SER A 398 SER A 399 GLY A 421 SITE 4 AC4 26 GLY A 423 ARG A 426 MG A 501 MG A 502 SITE 5 AC4 26 MG A 503 9V6 A 505 HOH A 611 HOH A 647 SITE 6 AC4 26 HOH A 649 HOH A 690 HOH A 693 HOH A 722 SITE 7 AC4 26 HOH A 757 HOH A 772 SITE 1 AC5 16 MET A 300 ALA A 302 LEU A 309 ARG A 330 SITE 2 AC5 16 MET A 344 ASN A 346 CYS A 348 PHE A 384 SITE 3 AC5 16 SER A 399 ASP A 408 ILE A 413 TRP A 417 SITE 4 AC5 16 GLY A 419 ALA A 420 ATP A 504 9V6 A 506 SITE 1 AC6 17 MET A 276 ALA A 302 LEU A 305 ALA A 306 SITE 2 AC6 17 LEU A 309 ASN A 346 CYS A 348 PHE A 384 SITE 3 AC6 17 SER A 399 VAL A 401 LEU A 407 ASP A 408 SITE 4 AC6 17 TRP A 411 ILE A 413 TRP A 417 GLY A 421 SITE 5 AC6 17 9V6 A 505 SITE 1 AC7 6 ASN A 203 PRO A 204 ASP A 206 HOH A 602 SITE 2 AC7 6 HOH A 619 HOH A 836 SITE 1 AC8 3 GLU A 341 ARG A 442 EDO A 510 SITE 1 AC9 5 ASP A 196 GLU A 199 VAL A 200 TYR A 446 SITE 2 AC9 5 HOH A 630 SITE 1 AD1 5 LEU A 339 GLU A 340 GLU A 341 LYS A 438 SITE 2 AD1 5 K A 508 SITE 1 AD2 4 LEU A 370 GLY A 371 HOH A 606 HOH A 677 CRYST1 101.419 43.887 72.386 90.00 119.45 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 0.009860 0.000000 0.005567 0.00000 SCALE2 0.000000 0.022786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015865 0.00000