HEADER TRANSLATION 22-JUL-18 6ABK TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED TITLE 2 WITH TEOCLYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRROLYSYL-TRNA SYNTHETASE,PYLRS; COMPND 5 EC: 6.1.1.26; COMPND 6 ENGINEERED: YES; COMPND 7 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, DU43_20175, DU67_18120; 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, TRNA, PYRROLYSYL- KEYWDS 2 TRNA SYNTHETASE, TRANSLATION EXPDTA X-RAY DIFFRACTION AUTHOR T.YANAGISAWA,M.KURATANI,S.YOKOYAMA REVDAT 4 22-NOV-23 6ABK 1 LINK REVDAT 3 07-AUG-19 6ABK 1 JRNL REVDAT 2 22-MAY-19 6ABK 1 SOURCE JRNL REVDAT 1 17-APR-19 6ABK 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. 1.58 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 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 34.9952 - 3.8075 0.99 2695 148 0.1530 0.1617 REMARK 3 2 3.8075 - 3.0227 1.00 2629 144 0.1491 0.1825 REMARK 3 3 3.0227 - 2.6407 1.00 2615 143 0.1677 0.2039 REMARK 3 4 2.6407 - 2.3994 1.00 2608 144 0.1714 0.1924 REMARK 3 5 2.3994 - 2.2274 1.00 2598 143 0.1577 0.2290 REMARK 3 6 2.2274 - 2.0961 1.00 2602 142 0.1520 0.1872 REMARK 3 7 2.0961 - 1.9911 1.00 2610 143 0.1540 0.1871 REMARK 3 8 1.9911 - 1.9045 1.00 2581 142 0.1524 0.1612 REMARK 3 9 1.9045 - 1.8312 1.00 2588 142 0.1653 0.1944 REMARK 3 10 1.8312 - 1.7680 1.00 2595 142 0.1671 0.2122 REMARK 3 11 1.7680 - 1.7127 1.00 2612 144 0.1665 0.2118 REMARK 3 12 1.7127 - 1.6637 1.00 2572 141 0.1660 0.1917 REMARK 3 13 1.6637 - 1.6199 1.00 2579 142 0.1803 0.2183 REMARK 3 14 1.6199 - 1.5804 0.99 2564 140 0.2081 0.2686 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.340 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 2323 REMARK 3 ANGLE : 1.915 3137 REMARK 3 CHIRALITY : 0.112 333 REMARK 3 PLANARITY : 0.012 404 REMARK 3 DIHEDRAL : 9.365 1976 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 122.5554 29.9311 27.9423 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.0606 REMARK 3 T33: 0.0747 T12: 0.0017 REMARK 3 T13: -0.0077 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.4292 L22: 0.1579 REMARK 3 L33: 0.3462 L12: -0.0402 REMARK 3 L13: 0.0366 L23: 0.1703 REMARK 3 S TENSOR REMARK 3 S11: -0.0690 S12: 0.0515 S13: 0.0159 REMARK 3 S21: -0.0261 S22: 0.0425 S23: 0.0286 REMARK 3 S31: -0.0198 S32: -0.1019 S33: -0.1065 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 6ABK 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_1300008448. 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 : 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 : 38450 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 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 (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 50.62250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.95300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.62250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.95300 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: 7060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 268.95342 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.55619 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 NH1 ARG A 314 O HOH A 601 1.89 REMARK 500 O HOH A 856 O HOH A 882 1.97 REMARK 500 O HOH A 694 O HOH A 798 1.97 REMARK 500 O HOH A 620 O HOH A 779 2.09 REMARK 500 N ARG A 239 O HOH A 602 2.15 REMARK 500 O HOH A 761 O HOH A 878 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 811 O HOH A 894 4756 2.03 REMARK 500 NZ LYS A 286 O HOH A 736 1565 2.08 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 THR A 195 CA - CB - CG2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ASP A 414 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 439 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TYR A 447 CB - CG - CD1 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 -55.59 -126.91 REMARK 500 ASP A 281 -141.52 31.95 REMARK 500 THR A 282 -110.80 -116.79 REMARK 500 GLU A 283 -126.99 21.16 REMARK 500 ASP A 292 -143.52 58.08 REMARK 500 ASP A 414 31.98 -142.34 REMARK 500 SER A 443 147.83 -171.08 REMARK 500 ASN A 453 77.75 -102.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 280 ASP A 281 143.60 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 895 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A 896 DISTANCE = 6.95 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 91.3 REMARK 620 3 ATP A 504 O1B 91.7 171.8 REMARK 620 4 ATP A 504 O1A 95.0 96.4 91.0 REMARK 620 5 HOH A 656 O 93.6 85.6 86.5 171.2 REMARK 620 6 HOH A 760 O 176.6 89.5 87.2 88.2 83.2 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 92.3 REMARK 620 3 ATP A 504 O1B 93.1 87.7 REMARK 620 4 HOH A 656 O 79.6 162.9 77.9 REMARK 620 5 HOH A 783 O 87.6 96.1 176.1 98.5 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 O2B REMARK 620 2 ATP A 504 O2G 91.0 REMARK 620 3 HOH A 650 O 93.5 92.9 REMARK 620 4 HOH A 663 O 177.6 91.2 85.4 REMARK 620 5 HOH A 737 O 87.1 178.0 87.6 90.8 REMARK 620 6 HOH A 747 O 92.9 87.6 173.5 88.1 92.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9VF 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 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE E444G IS A NATURAL MUTATION OBSERVED IN PYLRS GENE FROM REMARK 999 METHANOSARCINA MAZEI JCM9314 GENOME. DBREF1 6ABK A 185 454 UNP A0A0F8JXW8_METMZ DBREF2 6ABK A A0A0F8JXW8 185 454 SEQADV 6ABK GLY A 181 UNP A0A0F8JXW EXPRESSION TAG SEQADV 6ABK SER A 182 UNP A0A0F8JXW EXPRESSION TAG SEQADV 6ABK HIS A 183 UNP A0A0F8JXW EXPRESSION TAG SEQADV 6ABK MET A 184 UNP A0A0F8JXW EXPRESSION TAG SEQADV 6ABK ALA A 306 UNP A0A0F8JXW TYR 306 ENGINEERED MUTATION SEQADV 6ABK PHE A 384 UNP A0A0F8JXW TYR 384 ENGINEERED MUTATION SEQADV 6ABK GLY A 444 UNP A0A0F8JXW 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 9VF A 505 54 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 9VF (2S)-2-AZANYL-6-(TRIMETHYLSILYLMETHOXYCARBONYLAMINO) HETNAM 2 9VF HEXANOIC ACID FORMUL 2 MG 3(MG 2+) FORMUL 5 ATP C10 H16 N5 O13 P3 FORMUL 6 9VF C11 H24 N2 O4 SI FORMUL 7 HOH *296(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 GLU A 283 ILE A 288 5 6 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 CYS A 348 N ILE A 322 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 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 2.19 LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.27 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 2.12 LINK MG MG A 501 O HOH A 650 1555 1555 2.10 LINK MG MG A 501 O HOH A 663 1555 1555 2.14 LINK MG MG A 501 O HOH A 737 1555 1555 2.12 LINK MG MG A 501 O HOH A 747 1555 1555 2.06 LINK MG MG A 502 O1B ATP A 504 1555 1555 2.10 LINK MG MG A 502 O1A ATP A 504 1555 1555 2.12 LINK MG MG A 502 O HOH A 656 1555 1555 2.20 LINK MG MG A 502 O HOH A 760 1555 1555 2.16 LINK MG MG A 503 O1G ATP A 504 1555 1555 2.23 LINK MG MG A 503 O1B ATP A 504 1555 1555 2.33 LINK MG MG A 503 O HOH A 656 1555 1555 2.36 LINK MG MG A 503 O HOH A 783 1555 1555 2.09 CISPEP 1 ASP A 318 PRO A 319 0 3.35 CISPEP 2 GLY A 403 PRO A 404 0 -5.96 SITE 1 AC1 5 ATP A 504 HOH A 650 HOH A 663 HOH A 737 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 656 HOH A 760 SITE 1 AC3 5 GLU A 396 MG A 502 ATP A 504 HOH A 656 SITE 2 AC3 5 HOH A 783 SITE 1 AC4 28 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC4 28 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC4 28 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC4 28 ARG A 426 MG A 501 MG A 502 MG A 503 SITE 5 AC4 28 9VF A 505 HOH A 615 HOH A 633 HOH A 650 SITE 6 AC4 28 HOH A 656 HOH A 663 HOH A 737 HOH A 738 SITE 7 AC4 28 HOH A 746 HOH A 747 HOH A 760 HOH A 782 SITE 1 AC5 22 MET A 276 MET A 300 ALA A 302 ALA A 306 SITE 2 AC5 22 LEU A 309 ASN A 346 CYS A 348 CYS A 381 SITE 3 AC5 22 PHE A 384 SER A 399 VAL A 401 ILE A 405 SITE 4 AC5 22 LEU A 407 ASP A 408 TRP A 411 ILE A 413 SITE 5 AC5 22 TRP A 417 GLY A 419 ALA A 420 GLY A 421 SITE 6 AC5 22 ATP A 504 HOH A 760 CRYST1 101.245 43.906 72.451 90.00 118.69 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 0.009877 0.000000 0.005406 0.00000 SCALE2 0.000000 0.022776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015734 0.00000