HEADER TRANSLATION 18-JUL-18 6AAN TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH METZLYS 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 6AAN 1 LINK REVDAT 3 07-AUG-19 6AAN 1 JRNL REVDAT 2 22-MAY-19 6AAN 1 SOURCE JRNL REVDAT 1 17-APR-19 6AAN 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. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 43124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 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 35.0130 - 3.6356 0.92 2882 140 0.1800 0.2011 REMARK 3 2 3.6356 - 2.8862 0.99 3034 148 0.1711 0.2032 REMARK 3 3 2.8862 - 2.5214 0.99 3014 146 0.1913 0.1933 REMARK 3 4 2.5214 - 2.2910 0.99 2994 145 0.1848 0.2142 REMARK 3 5 2.2910 - 2.1268 0.98 2963 145 0.1695 0.1881 REMARK 3 6 2.1268 - 2.0014 0.98 2995 146 0.1784 0.2013 REMARK 3 7 2.0014 - 1.9012 0.98 2940 142 0.1771 0.2055 REMARK 3 8 1.9012 - 1.8184 0.98 2950 143 0.1948 0.2362 REMARK 3 9 1.8184 - 1.7484 0.98 2959 144 0.1977 0.2342 REMARK 3 10 1.7484 - 1.6881 0.97 2904 141 0.2004 0.2303 REMARK 3 11 1.6881 - 1.6353 0.97 2925 142 0.1983 0.2016 REMARK 3 12 1.6353 - 1.5886 0.97 2950 144 0.2149 0.2561 REMARK 3 13 1.5886 - 1.5467 0.96 2864 139 0.2193 0.2518 REMARK 3 14 1.5467 - 1.5090 0.91 2751 134 0.2486 0.2659 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.400 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 : 0.010 2282 REMARK 3 ANGLE : 1.316 3090 REMARK 3 CHIRALITY : 0.070 333 REMARK 3 PLANARITY : 0.007 397 REMARK 3 DIHEDRAL : 15.974 1419 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 6AAN 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_1300008428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-15 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 : 43126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 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 (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 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 50.74200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.03600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.74200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.03600 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: 8040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 -34.71492 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.61882 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 ILE A 278 REMARK 465 ASP A 279 REMARK 465 ASN A 280 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 678 O HOH A 685 1.96 REMARK 500 OD1 ASP A 292 O HOH A 601 2.08 REMARK 500 NH1 ARG A 275 O HOH A 602 2.10 REMARK 500 O HOH A 746 O HOH A 818 2.11 REMARK 500 O HOH A 804 O HOH A 813 2.13 REMARK 500 O HOH A 773 O HOH A 795 2.15 REMARK 500 O HOH A 685 O HOH A 713 2.17 REMARK 500 O HOH A 651 O HOH A 727 2.18 REMARK 500 OD2 ASP A 414 O HOH A 603 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 748 O HOH A 758 2556 2.07 REMARK 500 O HOH A 653 O HOH A 813 4455 2.08 REMARK 500 O HOH A 807 O HOH A 820 1556 2.17 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 298 NE - CZ - NH2 ANGL. DEV. = -3.4 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 62.64 -117.19 REMARK 500 GLU A 238 -53.21 -131.96 REMARK 500 TYR A 272 1.98 -60.80 REMARK 500 GLU A 274 25.01 -77.49 REMARK 500 SER A 285 -68.37 75.49 REMARK 500 ASP A 292 -131.20 55.89 REMARK 500 GLU A 332 126.79 -171.79 REMARK 500 ASP A 334 43.71 37.82 REMARK 500 ASP A 414 35.03 -141.30 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 829 DISTANCE = 7.13 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 85.8 REMARK 620 3 HOH A 617 O 100.4 53.6 REMARK 620 4 HOH A 636 O 128.4 62.3 92.0 REMARK 620 N 1 2 3 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 113.5 REMARK 620 3 HOH A 687 O 127.9 113.9 REMARK 620 4 HOH A 769 O 60.2 129.9 102.4 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 81.8 REMARK 620 3 ATP A 504 O1A 108.2 85.6 REMARK 620 4 ATP A 504 O1B 98.8 174.0 88.6 REMARK 620 5 HOH A 689 O 90.3 88.0 159.2 97.9 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 396 OE1 REMARK 620 2 ATP A 504 O1G 87.3 REMARK 620 3 ATP A 504 O1B 94.5 85.3 REMARK 620 4 HOH A 644 O 68.2 93.8 162.7 REMARK 620 5 HOH A 689 O 71.2 156.7 87.5 86.5 REMARK 620 N 1 2 3 4 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 92.4 REMARK 620 3 HOH A 613 O 93.3 90.1 REMARK 620 4 HOH A 620 O 99.4 167.7 85.8 REMARK 620 5 HOH A 633 O 90.1 85.3 174.4 98.0 REMARK 620 6 HOH A 643 O 172.1 81.4 81.9 86.5 94.2 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 9TX 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 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 6AAN A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 6AAN GLY A 181 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAN SER A 182 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAN HIS A 183 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAN MET A 184 UNP Q8PWY1 EXPRESSION TAG SEQADV 6AAN ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION SEQADV 6AAN PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION SEQADV 6AAN 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 9TX A 505 41 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 9TX N6-{[(3-ETHYNYLPHENYL)METHOXY]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 9TX C16 H20 N2 O4 FORMUL 7 K 2(K 1+) FORMUL 9 PEG C4 H10 O3 FORMUL 10 HOH *229(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 GLU A 271 ILE A 273 5 3 HELIX 5 AA5 LEU A 301 ASP A 313 1 13 HELIX 6 AA6 THR A 355 GLY A 371 1 17 HELIX 7 AA7 ILE A 405 GLY A 412 5 8 HELIX 8 AA8 LEU A 424 ASP A 433 1 10 HELIX 9 AA9 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 HIS A 392 O LEU A 395 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 2.99 LINK O ASP A 206 K K A 506 1555 1555 3.25 LINK OE1 GLU A 341 K K A 507 1555 1555 2.59 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.44 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.64 LINK OG SER A 399 MG MG A 502 1555 1555 2.17 LINK O ARG A 442 K K A 507 1555 1555 2.82 LINK MG MG A 501 O2G ATP A 504 1555 1555 2.00 LINK MG MG A 501 O2B ATP A 504 1555 1555 1.72 LINK MG MG A 501 O HOH A 613 1555 1555 2.16 LINK MG MG A 501 O HOH A 620 1555 1555 1.99 LINK MG MG A 501 O HOH A 633 1555 1555 2.09 LINK MG MG A 501 O HOH A 643 1555 1555 2.29 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.31 LINK MG MG A 502 O1B ATP A 504 1555 1555 1.85 LINK MG MG A 502 O HOH A 689 1555 4456 2.53 LINK MG MG A 503 O1G ATP A 504 1555 1555 2.02 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.49 LINK MG MG A 503 O HOH A 644 1555 1555 1.99 LINK MG MG A 503 O HOH A 689 1555 4456 2.33 LINK K K A 506 O HOH A 617 1555 1555 2.64 LINK K K A 506 O HOH A 636 1555 1555 3.10 LINK K K A 507 O HOH A 687 1555 1555 2.57 LINK K K A 507 O HOH A 769 1555 1555 3.48 CISPEP 1 ILE A 273 GLU A 274 0 2.45 CISPEP 2 ASP A 318 PRO A 319 0 -1.72 CISPEP 3 GLY A 403 PRO A 404 0 -2.92 SITE 1 AC1 5 ATP A 504 HOH A 613 HOH A 620 HOH A 633 SITE 2 AC1 5 HOH A 643 SITE 1 AC2 5 GLU A 396 SER A 399 MG A 503 ATP A 504 SITE 2 AC2 5 HOH A 689 SITE 1 AC3 6 GLU A 207 GLU A 396 MG A 502 ATP A 504 SITE 2 AC3 6 HOH A 644 HOH A 689 SITE 1 AC4 23 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC4 23 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC4 23 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC4 23 ARG A 426 MG A 501 MG A 502 MG A 503 SITE 5 AC4 23 9TX A 505 HOH A 613 HOH A 620 HOH A 633 SITE 6 AC4 23 HOH A 643 HOH A 644 HOH A 720 SITE 1 AC5 10 MET A 276 ALA A 306 ASN A 346 CYS A 348 SITE 2 AC5 10 PHE A 384 SER A 399 LEU A 407 ASP A 408 SITE 3 AC5 10 TRP A 417 ATP A 504 SITE 1 AC6 6 LEU A 202 ASN A 203 PRO A 204 ASP A 206 SITE 2 AC6 6 HOH A 617 HOH A 636 SITE 1 AC7 3 GLU A 341 ARG A 442 HOH A 687 SITE 1 AC8 2 ARG A 248 HOH A 759 CRYST1 101.484 44.072 72.474 90.00 118.62 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 0.009854 0.000000 0.005378 0.00000 SCALE2 0.000000 0.022690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015719 0.00000