HEADER TRANSLATION 22-JUL-18 6ABL TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH OBRZLYS 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 6ABL 1 LINK REVDAT 3 07-AUG-19 6ABL 1 JRNL REVDAT 2 22-MAY-19 6ABL 1 SOURCE JRNL REVDAT 1 17-APR-19 6ABL 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. 1.47 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 48022 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.160 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 35.0708 - 3.5419 0.98 3382 147 0.1362 0.1618 REMARK 3 2 3.5419 - 2.8117 1.00 3354 145 0.1497 0.1907 REMARK 3 3 2.8117 - 2.4564 1.00 3334 146 0.1699 0.2058 REMARK 3 4 2.4564 - 2.2318 1.00 3315 144 0.1582 0.2043 REMARK 3 5 2.2318 - 2.0719 1.00 3324 144 0.1553 0.2200 REMARK 3 6 2.0719 - 1.9497 0.99 3304 144 0.1658 0.1701 REMARK 3 7 1.9497 - 1.8521 0.99 3259 141 0.1642 0.2310 REMARK 3 8 1.8521 - 1.7715 0.99 3276 142 0.1711 0.2001 REMARK 3 9 1.7715 - 1.7033 0.99 3272 143 0.1764 0.2210 REMARK 3 10 1.7033 - 1.6445 0.99 3266 142 0.1730 0.2106 REMARK 3 11 1.6445 - 1.5931 0.98 3277 143 0.1766 0.2143 REMARK 3 12 1.5931 - 1.5475 0.98 3212 139 0.1793 0.2081 REMARK 3 13 1.5475 - 1.5068 0.98 3267 142 0.1943 0.2304 REMARK 3 14 1.5068 - 1.4700 0.97 3180 138 0.2281 0.2672 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) : 19.440 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 : 0.013 2339 REMARK 3 ANGLE : 1.461 3169 REMARK 3 CHIRALITY : 0.104 341 REMARK 3 PLANARITY : 0.009 409 REMARK 3 DIHEDRAL : 17.913 934 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): 56.326 11.433 51.314 REMARK 3 T TENSOR REMARK 3 T11: 0.1978 T22: 0.3166 REMARK 3 T33: 0.2078 T12: 0.0195 REMARK 3 T13: 0.0023 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 3.8529 L22: 2.7371 REMARK 3 L33: 3.9695 L12: 0.3410 REMARK 3 L13: -0.9208 L23: 0.0486 REMARK 3 S TENSOR REMARK 3 S11: -0.1353 S12: 0.1910 S13: -0.1687 REMARK 3 S21: -0.0184 S22: 0.0148 S23: 0.2016 REMARK 3 S31: 0.4038 S32: -0.4855 S33: 0.1503 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 237 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.277 3.393 54.268 REMARK 3 T TENSOR REMARK 3 T11: 0.2645 T22: 0.2670 REMARK 3 T33: 0.2192 T12: 0.0411 REMARK 3 T13: 0.0589 T23: 0.0669 REMARK 3 L TENSOR REMARK 3 L11: 7.7184 L22: 2.1671 REMARK 3 L33: 0.9711 L12: -3.9955 REMARK 3 L13: -2.6335 L23: 1.4861 REMARK 3 S TENSOR REMARK 3 S11: -0.3681 S12: -0.2632 S13: -0.4505 REMARK 3 S21: 0.2711 S22: 0.1208 S23: 0.2709 REMARK 3 S31: 0.2545 S32: -0.1061 S33: 0.3038 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 238 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.606 -0.503 31.516 REMARK 3 T TENSOR REMARK 3 T11: 0.1270 T22: 0.0973 REMARK 3 T33: 0.1718 T12: -0.0261 REMARK 3 T13: 0.0173 T23: 0.0110 REMARK 3 L TENSOR REMARK 3 L11: 1.7161 L22: 0.8995 REMARK 3 L33: 8.0790 L12: -0.3469 REMARK 3 L13: 0.6029 L23: 0.6470 REMARK 3 S TENSOR REMARK 3 S11: -0.0657 S12: -0.0857 S13: -0.1732 REMARK 3 S21: 0.1100 S22: -0.0418 S23: 0.0529 REMARK 3 S31: 0.3462 S32: -0.2281 S33: 0.1803 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 257 THROUGH 284 ) REMARK 3 ORIGIN FOR THE GROUP (A): 81.118 19.703 19.140 REMARK 3 T TENSOR REMARK 3 T11: 0.2431 T22: 0.1607 REMARK 3 T33: 0.2695 T12: -0.0075 REMARK 3 T13: -0.0138 T23: 0.0532 REMARK 3 L TENSOR REMARK 3 L11: 1.6381 L22: 1.9045 REMARK 3 L33: 2.3201 L12: -0.1099 REMARK 3 L13: -0.2368 L23: 0.3523 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: 0.2133 S13: 0.4217 REMARK 3 S21: -0.1769 S22: 0.0582 S23: 0.2356 REMARK 3 S31: -0.5154 S32: -0.1339 S33: -0.0035 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 285 THROUGH 329 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.799 16.229 19.146 REMARK 3 T TENSOR REMARK 3 T11: 0.1698 T22: 0.1413 REMARK 3 T33: 0.1490 T12: -0.0222 REMARK 3 T13: -0.0252 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 2.0808 L22: 2.1296 REMARK 3 L33: 2.4749 L12: -0.5469 REMARK 3 L13: -0.7114 L23: 0.7390 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: 0.2445 S13: 0.1937 REMARK 3 S21: -0.1628 S22: 0.0100 S23: -0.0417 REMARK 3 S31: -0.3222 S32: -0.1027 S33: -0.0363 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): 71.697 8.527 20.622 REMARK 3 T TENSOR REMARK 3 T11: 0.1133 T22: 0.1576 REMARK 3 T33: 0.1655 T12: 0.0039 REMARK 3 T13: -0.0247 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 1.3888 L22: 1.2812 REMARK 3 L33: 1.5334 L12: 0.9451 REMARK 3 L13: 0.1003 L23: 0.0460 REMARK 3 S TENSOR REMARK 3 S11: -0.1033 S12: 0.1283 S13: 0.0699 REMARK 3 S21: -0.0625 S22: 0.0355 S23: 0.1493 REMARK 3 S31: 0.0121 S32: -0.2143 S33: 0.0414 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 371 THROUGH 454 ) REMARK 3 ORIGIN FOR THE GROUP (A): 69.740 11.162 23.981 REMARK 3 T TENSOR REMARK 3 T11: 0.1436 T22: 0.1620 REMARK 3 T33: 0.1902 T12: 0.0113 REMARK 3 T13: -0.0095 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 1.1100 L22: 0.5529 REMARK 3 L33: 2.0536 L12: 0.2247 REMARK 3 L13: -0.2704 L23: 0.0087 REMARK 3 S TENSOR REMARK 3 S11: -0.1123 S12: 0.0912 S13: 0.0856 REMARK 3 S21: -0.0565 S22: 0.0673 S23: 0.0993 REMARK 3 S31: -0.1107 S32: -0.2634 S33: -0.0169 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 6ABL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008433. 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 MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48022 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 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 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 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 50.83550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.14050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.83550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.14050 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: 7110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 168.75254 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.89189 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 NH2 ARG A 409 O HOH A 601 2.12 REMARK 500 OE2 GLU A 238 O HOH A 602 2.13 REMARK 500 O ASP A 334 O HOH A 603 2.14 REMARK 500 O HOH A 717 O HOH A 816 2.16 REMARK 500 O HOH A 727 O HOH A 786 2.19 REMARK 500 O ASP A 281 O HOH A 604 2.19 REMARK 500 O HOH A 908 O HOH A 911 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 248 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES 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 -69.62 -107.79 REMARK 500 ASP A 281 -98.80 -60.11 REMARK 500 THR A 282 -139.02 -154.97 REMARK 500 GLU A 283 -110.95 67.64 REMARK 500 ASP A 292 -138.61 63.87 REMARK 500 ASP A 334 92.10 66.42 REMARK 500 ASN A 453 79.33 -101.14 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 911 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 912 DISTANCE = 6.24 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 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE2 REMARK 620 2 SER A 399 OG 93.2 REMARK 620 3 ATP A 504 O1A 97.1 94.5 REMARK 620 4 ATP A 504 O1B 91.2 173.8 89.2 REMARK 620 5 HOH A 674 O 94.2 88.6 168.0 86.7 REMARK 620 6 HOH A 793 O 177.5 87.9 85.1 87.5 83.5 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 O1G 93.4 REMARK 620 3 ATP A 504 O1B 94.1 83.9 REMARK 620 4 HOH A 674 O 79.2 161.0 79.2 REMARK 620 5 HOH A 771 O 84.2 102.9 173.1 93.9 REMARK 620 6 HOH A 796 O 172.3 93.8 83.9 93.1 96.8 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 O2B REMARK 620 2 ATP A 504 O2G 89.4 REMARK 620 3 HOH A 646 O 92.9 94.4 REMARK 620 4 HOH A 675 O 178.5 91.0 85.6 REMARK 620 5 HOH A 726 O 85.5 174.8 84.8 94.1 REMARK 620 6 HOH A 746 O 93.4 86.4 173.7 88.1 95.0 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 9VL 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 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 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 6ABL A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 6ABL GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABL SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABL HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABL MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 6ABL ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 6ABL PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 6ABL 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 9VL A 505 42 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 9VL (2S)-2-AZANYL-6-[(2-BROMOPHENYL) HETNAM 2 9VL METHOXYCARBONYLAMINO]HEXANOIC ACID FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 9VL C14 H19 BR N2 O4 FORMUL 7 HOH *312(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 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 LYS A 375 O MET A 391 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 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 2.14 LINK MG MG A 501 O2B ATP A 504 1555 1555 2.05 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.09 LINK MG MG A 501 O HOH A 646 1555 1555 2.15 LINK MG MG A 501 O HOH A 675 1555 1555 2.16 LINK MG MG A 501 O HOH A 726 1555 1555 2.07 LINK MG MG A 501 O HOH A 746 1555 1555 2.10 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.24 LINK MG MG A 502 O1B ATP A 504 1555 1555 2.16 LINK MG MG A 502 O HOH A 674 1555 1555 2.19 LINK MG MG A 502 O HOH A 793 1555 1555 2.20 LINK MG MG A 503 O1G ATP A 504 1555 1555 2.15 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.36 LINK MG MG A 503 O HOH A 674 1555 1555 2.33 LINK MG MG A 503 O HOH A 771 1555 1555 2.09 LINK MG MG A 503 O HOH A 796 1555 1555 2.15 CISPEP 1 ASP A 318 PRO A 319 0 -0.78 CISPEP 2 GLY A 403 PRO A 404 0 -1.26 SITE 1 AC1 5 ATP A 504 HOH A 646 HOH A 675 HOH A 726 SITE 2 AC1 5 HOH A 746 SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 6 HOH A 674 HOH A 793 SITE 1 AC3 6 GLU A 396 MG A 502 ATP A 504 HOH A 674 SITE 2 AC3 6 HOH A 771 HOH A 796 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 9VL A 505 HOH A 646 HOH A 653 HOH A 674 SITE 6 AC4 27 HOH A 675 HOH A 720 HOH A 726 HOH A 746 SITE 7 AC4 27 HOH A 753 HOH A 793 HOH A 796 SITE 1 AC5 18 MET A 276 ALA A 302 ALA A 306 LEU A 309 SITE 2 AC5 18 MET A 344 ASN A 346 CYS A 348 PHE A 384 SITE 3 AC5 18 SER A 399 LEU A 407 ASP A 408 TRP A 411 SITE 4 AC5 18 ILE A 413 TRP A 417 GLY A 419 GLY A 421 SITE 5 AC5 18 ATP A 504 HOH A 736 CRYST1 101.671 44.281 72.654 90.00 118.43 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 0.009836 0.000000 0.005326 0.00000 SCALE2 0.000000 0.022583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015652 0.00000