HEADER LIGASE 19-DEC-23 8RIS TITLE COMPUTATIONALLY REDESIGEND VARIANT OF PYRROLYSYL-TRNA SYNTHETASE TITLE 2 (Y306A) 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 2209; SOURCE 4 GENE: PYLS, MM_1445; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PYRROLYSYL-TRNA SYNTHETASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR G.OBERDORFER,M.MOSER,D.STOLL REVDAT 1 01-JAN-25 8RIS 0 JRNL AUTH G.OBERDORFER,M.MOSER,D.STOLL JRNL TITL COMPUTATIONALLY REDESIGEND VARIANT OF PYRROLYSYL-TRNA JRNL TITL 2 SYNTHETASE (Y306A) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 609 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 45.1700 - 4.2900 1.00 2945 156 0.1943 0.2246 REMARK 3 2 4.2800 - 3.4000 1.00 2879 151 0.2020 0.2207 REMARK 3 3 3.4000 - 2.9700 1.00 2866 151 0.2600 0.2729 REMARK 3 4 2.9700 - 2.7000 1.00 2874 151 0.3316 0.3775 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.461 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.992 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.82 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 : 0.001 2175 REMARK 3 ANGLE : 0.402 2931 REMARK 3 CHIRALITY : 0.039 321 REMARK 3 PLANARITY : 0.004 384 REMARK 3 DIHEDRAL : 8.176 833 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 8RIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292134757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873128 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.21660 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 18.20 REMARK 200 R MERGE FOR SHELL (I) : 3.11200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.970 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M L-ARGININE, 0.05M L-GLUTAMIC REMARK 280 ACID MONOSODIUM SALT HYDRATE, 28% V/V PEG SMEAR BROAD, 5% V/V REMARK 280 GLYCEROL, DROP RATIO 1:1, PH 7.9, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.60233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.20467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.60233 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.20467 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: MONOMERIC 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 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 185 REMARK 465 SER A 186 REMARK 465 HIS A 187 REMARK 465 ASN A 211 REMARK 465 SER A 333 REMARK 465 ASP A 334 REMARK 465 SER A 380 REMARK 465 CYS A 381 REMARK 465 MET A 382 REMARK 465 VAL A 383 REMARK 465 TYR A 384 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 GLU A 271 CG CD OE1 OE2 REMARK 470 ASN A 280 CG OD1 ND2 REMARK 470 ASP A 281 CG OD1 OD2 REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 LEU A 284 CG CD1 CD2 REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 ARG A 330 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 GLU A 337 CG CD OE1 OE2 REMARK 470 LYS A 375 CG CD CE NZ REMARK 470 LYS A 435 CG CD CE NZ 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 56.84 -107.29 REMARK 500 GLU A 237 -80.36 -127.91 REMARK 500 ASN A 280 -134.64 58.97 REMARK 500 VAL A 291 -73.23 -101.64 REMARK 500 ASN A 294 -35.26 -131.39 REMARK 500 ALA A 315 -33.77 -134.12 REMARK 500 LYS A 336 -158.40 -109.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 8RIS A 188 454 UNP Q8PWY1 PYLS_METMA 188 454 SEQADV 8RIS GLY A 185 UNP Q8PWY1 EXPRESSION TAG SEQADV 8RIS SER A 186 UNP Q8PWY1 EXPRESSION TAG SEQADV 8RIS HIS A 187 UNP Q8PWY1 EXPRESSION TAG SEQADV 8RIS ALA A 306 UNP Q8PWY1 TYR 306 CONFLICT SEQRES 1 A 270 GLY SER HIS PRO ALA LEU THR LYS SER GLN THR ASP ARG SEQRES 2 A 270 LEU GLU VAL LEU LEU ASN PRO LYS ASP GLU ILE SER LEU SEQRES 3 A 270 ASN SER GLY LYS PRO PHE ARG GLU LEU GLU SER GLU LEU SEQRES 4 A 270 LEU SER ARG ARG LYS LYS ASP LEU GLN GLN ILE TYR ALA SEQRES 5 A 270 GLU GLU ARG GLU ASN TYR LEU GLY LYS LEU GLU ARG GLU SEQRES 6 A 270 ILE THR ARG PHE PHE VAL ASP ARG GLY PHE LEU GLU ILE SEQRES 7 A 270 LYS SER PRO ILE LEU ILE PRO LEU GLU TYR ILE GLU ARG SEQRES 8 A 270 MET GLY ILE ASP ASN ASP THR GLU LEU SER LYS GLN ILE SEQRES 9 A 270 PHE ARG VAL ASP LYS ASN PHE CYS LEU ARG PRO MET LEU SEQRES 10 A 270 ALA PRO ASN LEU ALA ASN TYR LEU ARG LYS LEU ASP ARG SEQRES 11 A 270 ALA LEU PRO ASP PRO ILE LYS ILE PHE GLU ILE GLY PRO SEQRES 12 A 270 CYS TYR ARG LYS GLU SER ASP GLY LYS GLU HIS LEU GLU SEQRES 13 A 270 GLU PHE THR MET LEU ASN PHE CYS GLN MET GLY SER GLY SEQRES 14 A 270 CYS THR ARG GLU ASN LEU GLU SER ILE ILE THR ASP PHE SEQRES 15 A 270 LEU ASN HIS LEU GLY ILE ASP PHE LYS ILE VAL GLY ASP SEQRES 16 A 270 SER CYS MET VAL TYR GLY ASP THR LEU ASP VAL MET HIS SEQRES 17 A 270 GLY ASP LEU GLU LEU SER SER ALA VAL VAL GLY PRO ILE SEQRES 18 A 270 PRO LEU ASP ARG GLU TRP GLY ILE ASP LYS PRO TRP ILE SEQRES 19 A 270 GLY ALA GLY PHE GLY LEU GLU ARG LEU LEU LYS VAL LYS SEQRES 20 A 270 HIS ASP PHE LYS ASN ILE LYS ARG ALA ALA ARG SER GLU SEQRES 21 A 270 SER TYR TYR ASN GLY ILE SER THR ASN LEU HET 1PE A 501 16 HET NA A 502 1 HET GOL A 503 6 HET GOL A 504 6 HET EDO A 505 4 HET EDO A 506 4 HET EDO A 507 4 HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN 1PE PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 1PE C10 H22 O6 FORMUL 3 NA NA 1+ FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 EDO 3(C2 H6 O2) FORMUL 9 HOH *65(H2 O) HELIX 1 AA1 THR A 191 LEU A 201 1 11 HELIX 2 AA2 PRO A 215 GLU A 237 1 23 HELIX 3 AA3 ASN A 241 ASP A 256 1 16 HELIX 4 AA4 LEU A 270 ARG A 275 1 6 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 HIS A 432 1 9 HELIX 9 AA9 ASN A 436 ALA A 440 5 5 SHEET 1 AA1 4 LEU A 260 ILE A 262 0 SHEET 2 AA1 4 ILE A 320 TYR A 329 1 O PHE A 323 N ILE A 262 SHEET 3 AA1 4 GLU A 341 MET A 350 -1 O MET A 344 N GLY A 326 SHEET 4 AA1 4 TRP A 417 GLY A 423 -1 O PHE A 422 N LEU A 345 SHEET 1 AA2 2 LEU A 267 PRO A 269 0 SHEET 2 AA2 2 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 1 AA3 3 LYS A 375 VAL A 377 0 SHEET 2 AA3 3 THR A 387 HIS A 392 -1 O ASP A 389 N VAL A 377 SHEET 3 AA3 3 LEU A 395 VAL A 401 -1 O LEU A 397 N VAL A 390 SHEET 1 AA4 2 TYR A 446 TYR A 447 0 SHEET 2 AA4 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447 LINK OD1 ASP A 386 NA NA A 502 1555 1555 3.13 CISPEP 1 ASP A 318 PRO A 319 0 -0.96 CRYST1 104.306 104.306 70.807 90.00 90.00 120.00 P 64 6 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 0.009587 0.005535 0.000000 0.00000 SCALE2 0.000000 0.011070 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014123 0.00000