HEADER TRANSLATION 18-JUL-18 6AAO TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH TCO*LYS 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 6AAO 1 LINK REVDAT 3 07-AUG-19 6AAO 1 JRNL REVDAT 2 22-MAY-19 6AAO 1 SOURCE JRNL REVDAT 1 17-APR-19 6AAO 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 1.9_1690 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) : 35.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 53199 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 35.1364 - 3.3814 1.00 3908 153 0.1473 0.1798 REMARK 3 2 3.3814 - 2.6842 1.00 3836 149 0.1651 0.2248 REMARK 3 3 2.6842 - 2.3450 1.00 3826 149 0.1660 0.2199 REMARK 3 4 2.3450 - 2.1306 1.00 3763 148 0.1497 0.1866 REMARK 3 5 2.1306 - 1.9779 1.00 3801 148 0.1512 0.1914 REMARK 3 6 1.9779 - 1.8613 1.00 3803 149 0.1526 0.1946 REMARK 3 7 1.8613 - 1.7681 1.00 3773 147 0.1537 0.1813 REMARK 3 8 1.7681 - 1.6911 1.00 3780 147 0.1480 0.1879 REMARK 3 9 1.6911 - 1.6260 1.00 3789 149 0.1345 0.1895 REMARK 3 10 1.6260 - 1.5699 1.00 3758 147 0.1300 0.1814 REMARK 3 11 1.5699 - 1.5208 1.00 3797 148 0.1382 0.2035 REMARK 3 12 1.5208 - 1.4774 1.00 3763 146 0.1373 0.1755 REMARK 3 13 1.4774 - 1.4385 0.95 3605 141 0.1397 0.2101 REMARK 3 14 1.4385 - 1.4034 0.52 1998 78 0.1456 0.2007 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.040 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 : 0.018 2330 REMARK 3 ANGLE : 1.746 3155 REMARK 3 CHIRALITY : 0.096 339 REMARK 3 PLANARITY : 0.009 407 REMARK 3 DIHEDRAL : 15.814 931 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6AAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008429. 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 : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54493 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.3000 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 (%): 45.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 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 50.79400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.98550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.79400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.98550 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: 8580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 168.22275 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.79054 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 OE2 GLU A 199 O HOH A 601 2.04 REMARK 500 NH2 ARG A 356 O HOH A 602 2.05 REMARK 500 O HOH A 801 O HOH A 821 2.09 REMARK 500 O HOH A 615 O HOH A 810 2.10 REMARK 500 O HOH A 613 O HOH A 747 2.11 REMARK 500 O HOH A 738 O HOH A 803 2.12 REMARK 500 O HOH A 612 O HOH A 747 2.12 REMARK 500 O HOH A 804 O HOH A 883 2.15 REMARK 500 O HOH A 671 O HOH A 726 2.17 REMARK 500 NH2 ARG A 257 O HOH A 603 2.18 REMARK 500 OE1 GLU A 238 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 847 O HOH A 890 4646 2.12 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 LEU A 284 CA - CB - CG ANGL. DEV. = 14.3 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 207 68.89 -113.74 REMARK 500 GLU A 238 -64.06 -123.85 REMARK 500 ASP A 292 -142.29 52.09 REMARK 500 SER A 443 140.28 -171.10 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 892 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 893 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A 894 DISTANCE = 6.92 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 ASN A 203 O REMARK 620 2 ASP A 206 O 84.3 REMARK 620 3 HOH A 606 O 102.0 45.7 REMARK 620 4 HOH A 608 O 123.0 63.6 88.1 REMARK 620 5 HOH A 842 O 85.2 161.7 122.7 134.6 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 73.3 REMARK 620 3 ATP A 504 O1B 71.8 3.2 REMARK 620 4 ATP A 504 O1G 68.2 5.1 4.6 REMARK 620 5 HOH A 634 O 74.9 1.7 4.6 6.7 REMARK 620 6 HOH A 748 O 71.6 4.6 7.1 5.5 4.9 REMARK 620 N 1 2 3 4 5 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 GLU A 341 OE1 REMARK 620 2 ARG A 442 O 111.2 REMARK 620 3 HOH A 808 O 116.2 131.1 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 90.9 REMARK 620 3 ATP A 504 O1B 89.0 171.4 REMARK 620 4 ATP A 504 O1A 93.6 95.8 92.9 REMARK 620 5 HOH A 634 O 88.9 89.8 81.5 173.9 REMARK 620 6 HOH A 751 O 176.0 89.7 89.8 90.3 87.2 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 88.3 REMARK 620 3 HOH A 647 O 93.3 91.2 REMARK 620 4 HOH A 710 O 94.1 177.5 87.9 REMARK 620 5 HOH A 740 O 178.3 90.2 85.8 87.3 REMARK 620 6 HOH A 762 O 89.5 88.7 177.2 92.0 91.4 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 9U0 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 PEG 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 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 6AAO A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 6AAO GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAO SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAO HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAO MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAO ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 6AAO PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 6AAO 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 9U0 A 505 21 HET K A 506 1 HET K A 507 1 HET PEG A 508 7 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 9U0 N6-({[(1S,2E)-CYCLOOCT-2-EN-1-YL]OXY}CARBONYL)-L-LYSINE HETNAM K POTASSIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 9U0 C15 H26 N2 O4 FORMUL 7 K 2(K 1+) FORMUL 9 PEG C4 H10 O3 FORMUL 10 HOH *294(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 ASN A 203 K K A 506 1555 1555 3.06 LINK O ASP A 206 K K A 506 1555 1555 3.19 LINK OE2 GLU A 207 MG MG A 503 1555 4646 2.07 LINK OE1 GLU A 341 K K A 507 1555 1555 2.66 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.12 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.15 LINK OG SER A 399 MG MG A 502 1555 1555 2.09 LINK O ARG A 442 K K A 507 1555 1555 2.76 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.12 LINK MG MG A 501 O2B ATP A 504 1555 1555 2.11 LINK MG MG A 501 O HOH A 647 1555 1555 2.11 LINK MG MG A 501 O HOH A 710 1555 1555 2.07 LINK MG MG A 501 O HOH A 740 1555 1555 2.11 LINK MG MG A 501 O HOH A 762 1555 1555 2.14 LINK MG MG A 502 O1B ATP A 504 1555 1555 2.08 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.03 LINK MG MG A 502 O HOH A 634 1555 1555 2.18 LINK MG MG A 502 O HOH A 751 1555 1555 2.13 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.22 LINK MG MG A 503 O1G ATP A 504 1555 1555 2.09 LINK MG MG A 503 O HOH A 634 1555 1555 2.19 LINK MG MG A 503 O HOH A 748 1555 1555 2.14 LINK K K A 506 O HOH A 606 1555 1555 2.61 LINK K K A 506 O HOH A 608 1555 1555 2.90 LINK K K A 506 O HOH A 842 1555 1555 2.90 LINK K K A 507 O HOH A 808 1555 1555 3.44 CISPEP 1 ASP A 318 PRO A 319 0 -2.76 CISPEP 2 GLY A 403 PRO A 404 0 -2.05 SITE 1 AC1 5 ATP A 504 HOH A 647 HOH A 710 HOH A 740 SITE 2 AC1 5 HOH A 762 SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 6 HOH A 634 HOH A 751 SITE 1 AC3 6 GLU A 207 GLU A 396 MG A 502 ATP A 504 SITE 2 AC3 6 HOH A 634 HOH A 748 SITE 1 AC4 27 GLU A 207 ARG A 330 GLU A 332 HIS A 338 SITE 2 AC4 27 LEU A 339 PHE A 342 MET A 344 GLU A 396 SITE 3 AC4 27 LEU A 397 SER A 398 SER A 399 GLY A 421 SITE 4 AC4 27 GLY A 423 ARG A 426 MG A 501 MG A 502 SITE 5 AC4 27 MG A 503 9U0 A 505 HOH A 615 HOH A 634 SITE 6 AC4 27 HOH A 647 HOH A 710 HOH A 740 HOH A 751 SITE 7 AC4 27 HOH A 755 HOH A 762 HOH A 772 SITE 1 AC5 17 ALA A 302 LEU A 305 ALA A 306 MET A 344 SITE 2 AC5 17 ASN A 346 CYS A 348 PHE A 384 SER A 399 SITE 3 AC5 17 ASP A 408 ILE A 413 TRP A 417 GLY A 419 SITE 4 AC5 17 ALA A 420 GLY A 421 ATP A 504 HOH A 637 SITE 5 AC5 17 HOH A 745 SITE 1 AC6 6 ASN A 203 PRO A 204 ASP A 206 HOH A 606 SITE 2 AC6 6 HOH A 608 HOH A 842 SITE 1 AC7 2 GLU A 341 ARG A 442 SITE 1 AC8 8 SER A 333 ASP A 334 GLY A 335 LYS A 336 SITE 2 AC8 8 GLU A 337 HIS A 338 HOH A 768 HOH A 889 CRYST1 101.588 43.971 72.739 90.00 118.72 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 0.009844 0.000000 0.005394 0.00000 SCALE2 0.000000 0.022742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015677 0.00000