HEADER LYASE 18-OCT-25 9X7W TITLE O-ACETYLSERINE(THIOL)LYASE 2 (OASTL2) FROM DURIO ZIBETHINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.5.1.47; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DURIO ZIBETHINUS; SOURCE 3 ORGANISM_TAXID: 66656; SOURCE 4 GENE: LOC111279271; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS O-ACETYLSERINE(THIOL)LYASE, SULFUR METABOLISM, DURIO ZIBETHINUS, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR P.WILASLUCK,K.WANGKANONT REVDAT 1 28-OCT-26 9X7W 0 JRNL AUTH P.WILASLUCK,K.WANGKANONT JRNL TITL O-ACETYLSERINE(THIOL)LYASE 2 (OASTL2) FROM DURIO ZIBETHINUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1173 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 29.0500 - 3.9000 1.00 2974 176 0.1572 0.1884 REMARK 3 2 3.9000 - 3.1000 1.00 2880 154 0.2109 0.2408 REMARK 3 3 3.0900 - 2.7000 0.99 2845 134 0.2413 0.2946 REMARK 3 4 2.7000 - 2.4600 0.99 2795 156 0.2689 0.3324 REMARK 3 5 2.4600 - 2.2800 0.98 2781 140 0.2292 0.2830 REMARK 3 6 2.2800 - 2.1500 0.98 2751 156 0.2929 0.3429 REMARK 3 7 2.1500 - 2.0400 0.98 2748 137 0.3317 0.3981 REMARK 3 8 2.0400 - 1.9500 0.97 2761 120 0.3828 0.4468 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) : 0.249 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.63 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 : 0.007 2385 REMARK 3 ANGLE : 0.931 3226 REMARK 3 CHIRALITY : 0.053 376 REMARK 3 PLANARITY : 0.008 413 REMARK 3 DIHEDRAL : 15.621 896 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 9X7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300064582. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999873 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 : MOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.8.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24057 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 29.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.60 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.10 REMARK 200 R MERGE FOR SHELL (I) : 1.37400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS HCL, 21% PEG 3,350, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 64.79067 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 32.39533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.39533 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 64.79067 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 577 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 GLN A 4 REMARK 465 SER A 5 REMARK 465 THR A 322 REMARK 465 PHE A 323 REMARK 465 GLU A 324 REMARK 465 PRO A 325 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 ARG A 93 60.10 64.52 REMARK 500 THR A 163 -54.97 -120.03 REMARK 500 SER A 307 35.71 -98.58 REMARK 500 SER A 313 3.77 -64.72 REMARK 500 VAL A 314 4.80 -66.31 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9X7W A 1 325 UNP A0A6P5X2C9_DURZI DBREF2 9X7W A A0A6P5X2C9 1 325 SEQADV 9X7W GLY A 0 UNP A0A6P5X2C EXPRESSION TAG SEQADV 9X7W GLN A 4 UNP A0A6P5X2C GLU 4 CONFLICT SEQRES 1 A 326 GLY MET ALA HIS GLN SER ILE GLY ILE ALA ARG ASP VAL SEQRES 2 A 326 THR GLU LEU ILE GLY LYS THR PRO LEU VAL TYR LEU ASN SEQRES 3 A 326 ASN VAL VAL ASP GLY CYS VAL ALA ARG ILE ALA ALA LYS SEQRES 4 A 326 LEU GLU MET MET GLU PRO CYS SER SER VAL LLP ASP ARG SEQRES 5 A 326 ILE GLY TYR SER MET ILE ALA ASP ALA GLU ALA LYS GLY SEQRES 6 A 326 LEU ILE THR PRO GLY LYS SER VAL LEU ILE GLU PRO THR SEQRES 7 A 326 SER GLY ASN THR GLY ILE GLY LEU ALA PHE MET ALA ALA SEQRES 8 A 326 ALA LYS ARG TYR ARG LEU ILE ILE THR MET PRO ALA SER SEQRES 9 A 326 MET SER LEU GLU ARG ARG ILE ILE LEU ARG ALA PHE GLY SEQRES 10 A 326 ALA GLU LEU VAL LEU THR ASP PRO ALA LYS GLY MET LYS SEQRES 11 A 326 GLY ALA VAL GLN LYS ALA GLU GLU ILE LEU ALA LYS THR SEQRES 12 A 326 PRO ASN ALA TYR MET LEU GLN GLN PHE GLU ASN PRO ALA SEQRES 13 A 326 ASN PRO LYS ILE HIS TYR GLU THR THR GLY PRO GLU LEU SEQRES 14 A 326 TRP LYS GLY SER GLY GLY LYS ILE ASP ALA LEU VAL SER SEQRES 15 A 326 GLY ILE GLY THR GLY GLY THR ILE THR GLY ALA GLY LYS SEQRES 16 A 326 TYR LEU LYS GLU GLN ASN PRO ASN ILE LYS LEU TYR GLY SEQRES 17 A 326 VAL GLU PRO VAL GLU SER PRO VAL LEU ALA GLY GLY LYS SEQRES 18 A 326 PRO GLY PRO HIS LYS ILE GLN GLY ILE GLY ALA GLY PHE SEQRES 19 A 326 ILE PRO GLY VAL LEU GLU VAL ASN ILE VAL ASP GLU VAL SEQRES 20 A 326 VAL GLN VAL SER SER ASP GLU ALA ILE GLU THR ALA LYS SEQRES 21 A 326 LEU LEU ALA LEU LYS GLU GLY LEU LEU VAL GLY ILE SER SEQRES 22 A 326 SER GLY ALA ALA THR ALA ALA ALA ILE LYS ILE ALA LYS SEQRES 23 A 326 ARG PRO GLU ASN ALA GLY LYS LEU ILE VAL ALA ILE PHE SEQRES 24 A 326 PRO SER PHE GLY GLU ARG TYR LEU SER SER VAL LEU PHE SEQRES 25 A 326 GLU SER VAL ARG LYS GLU ALA GLU SER MET THR PHE GLU SEQRES 26 A 326 PRO MODRES 9X7W LLP A 49 LYS MODIFIED RESIDUE HET LLP A 49 24 HET CL A 401 1 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM CL CHLORIDE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 CL CL 1- FORMUL 3 HOH *77(H2 O) HELIX 1 AA1 ASP A 11 ILE A 16 5 6 HELIX 2 AA2 MET A 41 GLU A 43 5 3 HELIX 3 AA3 VAL A 48 GLY A 64 1 17 HELIX 4 AA4 GLY A 79 ARG A 93 1 15 HELIX 5 AA5 SER A 105 PHE A 115 1 11 HELIX 6 AA6 LYS A 126 THR A 142 1 17 HELIX 7 AA7 PRO A 154 THR A 163 1 10 HELIX 8 AA8 THR A 163 SER A 172 1 10 HELIX 9 AA9 GLY A 186 ASN A 200 1 15 HELIX 10 AB1 GLU A 239 VAL A 243 5 5 HELIX 11 AB2 SER A 250 GLU A 265 1 16 HELIX 12 AB3 GLY A 270 LYS A 285 1 16 HELIX 13 AB4 ARG A 286 ALA A 290 5 5 HELIX 14 AB5 PHE A 301 LEU A 306 5 6 HELIX 15 AB6 PHE A 311 ARG A 315 5 5 SHEET 1 AA1 6 LEU A 21 TYR A 23 0 SHEET 2 AA1 6 ARG A 34 LEU A 39 -1 O ALA A 37 N VAL A 22 SHEET 3 AA1 6 LEU A 293 PHE A 298 1 O PHE A 298 N LYS A 38 SHEET 4 AA1 6 ALA A 178 GLY A 182 1 N VAL A 180 O VAL A 295 SHEET 5 AA1 6 LYS A 204 PRO A 210 1 O TYR A 206 N LEU A 179 SHEET 6 AA1 6 GLU A 245 VAL A 249 1 O VAL A 247 N GLY A 207 SHEET 1 AA2 4 GLU A 118 THR A 122 0 SHEET 2 AA2 4 ARG A 95 PRO A 101 1 N ILE A 98 O GLU A 118 SHEET 3 AA2 4 VAL A 72 PRO A 76 1 N LEU A 73 O ILE A 97 SHEET 4 AA2 4 ALA A 145 MET A 147 1 O TYR A 146 N VAL A 72 LINK C VAL A 48 N LLP A 49 1555 1555 1.33 LINK C LLP A 49 N ASP A 50 1555 1555 1.33 CRYST1 75.748 75.748 97.186 90.00 90.00 120.00 P 32 2 1 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 0.013202 0.007622 0.000000 0.00000 SCALE2 0.000000 0.015244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010290 0.00000 CONECT 313 333 CONECT 318 319 326 CONECT 319 318 320 321 CONECT 320 319 CONECT 321 319 322 323 CONECT 322 321 CONECT 323 321 324 325 CONECT 324 323 339 CONECT 325 323 326 327 CONECT 326 318 325 CONECT 327 325 328 CONECT 328 327 329 CONECT 329 328 330 331 332 CONECT 330 329 CONECT 331 329 CONECT 332 329 CONECT 333 313 334 CONECT 334 333 335 340 CONECT 335 334 336 CONECT 336 335 337 CONECT 337 336 338 CONECT 338 337 339 CONECT 339 324 338 CONECT 340 334 341 342 CONECT 341 340 CONECT 342 340 MASTER 254 0 2 15 10 0 0 6 2426 1 26 26 END