HEADER DE NOVO PROTEIN 28-JUN-24 9FW7 TITLE RETROALDOLASE 32 (RAD32) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETROALDOLASE 32 (RAD32); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RETROALDOLASE, DE NOVO ENZYME, RFDIFFUSION, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.BIJELIC,M.BRAUN,D.STOLL,A.TRIPP,M.CHAKATOK,G.OBERDORFER REVDAT 3 17-DEC-25 9FW7 1 JRNL REVDAT 2 10-DEC-25 9FW7 1 JRNL REVDAT 1 09-JUL-25 9FW7 0 JRNL AUTH M.BRAUN,A.TRIPP,M.CHAKATOK,S.KALTENBRUNNER,C.FISCHER, JRNL AUTH 2 D.STOLL,A.BIJELIC,W.ELAILY,M.G.TOTARO,M.MOSER,S.Y.HOCH, JRNL AUTH 3 H.LECHNER,F.ROSSI,M.ALEOTTI,M.HALL,G.OBERDORFER JRNL TITL COMPUTATIONAL ENZYME DESIGN BY CATALYTIC MOTIF SCAFFOLDING. JRNL REF NATURE 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 41339546 JRNL DOI 10.1038/S41586-025-09747-9 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21_5207: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 32.4500 - 3.1800 1.00 2696 142 0.1969 0.2439 REMARK 3 2 3.1700 - 2.5200 1.00 2719 143 0.2366 0.2995 REMARK 3 3 2.5200 - 2.2000 1.00 2718 143 0.2260 0.2897 REMARK 3 4 2.2000 - 2.0000 1.00 2722 144 0.2595 0.3376 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.460 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 : 0.002 1524 REMARK 3 ANGLE : 0.517 2065 REMARK 3 CHIRALITY : 0.034 248 REMARK 3 PLANARITY : 0.003 261 REMARK 3 DIHEDRAL : 19.422 559 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 9FW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292139841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96770 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15322 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 32.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MIB (SODIUM MALONATE DIBASIC REMARK 280 MONOHYDRATE, IMIDAZOLE, AND BORIC ACID), 15% PEG1500, PH 4.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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 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 13.77333 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 27.54667 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 MET A 1 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 LEU A 2 CG CD1 CD2 REMARK 470 GLU A 3 CG CD OE1 OE2 REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 GLU A 18 CG CD OE1 OE2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 GLU A 39 CG CD OE1 OE2 REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LEU A 90 CG CD1 CD2 REMARK 470 GLN A 119 CG CD OE1 NE2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 GLU A 158 CG CD OE1 OE2 REMARK 470 GLU A 162 CG CD OE1 OE2 REMARK 470 GLU A 183 CG CD OE1 OE2 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 3 -46.89 65.28 REMARK 500 LYS A 4 4.53 -66.39 REMARK 500 ASN A 159 46.87 -96.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9FW5 RELATED DB: PDB DBREF 9FW7 A 1 200 PDB 9FW7 9FW7 1 200 SEQRES 1 A 200 MET LEU GLU LYS ALA LYS GLU ALA ILE LYS GLU ALA ILE SEQRES 2 A 200 GLU ASN ARG ASP GLU LEU VAL GLU PRO TYR VAL GLU ARG SEQRES 3 A 200 ALA LYS LYS LEU ALA GLU GLU ILE LYS LYS TYR VAL GLU SEQRES 4 A 200 GLY GLY VAL GLU ALA ILE VAL GLU ALA ILE LYS ASN GLY SEQRES 5 A 200 ASP LEU GLU VAL LEU ALA MET LEU LEU LYS GLY ILE PHE SEQRES 6 A 200 TYR HIS GLY PHE TYR GLY GLU ARG GLU GLU ALA ILE GLU SEQRES 7 A 200 LEU LEU GLU LYS LEU ALA LYS ALA VAL LYS ASN LEU GLU SEQRES 8 A 200 GLN ARG LEU MET SER LEU LEU TYR ALA GLU LEU LEU ARG SEQRES 9 A 200 TYR MET GLU GLU LYS GLY ILE SER TRP GLU GLU PHE ALA SEQRES 10 A 200 PRO GLN TYR LEU THR LEU ILE THR ILE LEU LEU PRO THR SEQRES 11 A 200 TYR GLU LYS LEU LYS GLU ALA GLY VAL VAL THR GLU SER SEQRES 12 A 200 THR SER LEU GLU GLU LEU ARG GLU ILE ILE LYS LEU VAL SEQRES 13 A 200 LEU GLU ASN LEU PRO GLU PRO SER GLU LEU GLU LYS GLU SEQRES 14 A 200 ALA THR LYS GLU VAL GLU PRO ILE ASN LYS LYS MET GLY SEQRES 15 A 200 GLU TYR LEU SER PHE GLU GLU LEU LYS GLU VAL VAL GLU SEQRES 16 A 200 GLY VAL ALA ASN GLY FORMUL 2 HOH *39(H2 O) HELIX 1 AA1 ALA A 5 ASN A 15 1 11 HELIX 2 AA2 ARG A 16 GLU A 18 5 3 HELIX 3 AA3 LEU A 19 GLY A 41 1 23 HELIX 4 AA4 GLY A 41 ASN A 51 1 11 HELIX 5 AA5 ASP A 53 GLY A 68 1 16 HELIX 6 AA6 PHE A 69 GLY A 71 5 3 HELIX 7 AA7 GLU A 72 VAL A 87 1 16 HELIX 8 AA8 ASN A 89 GLY A 110 1 22 HELIX 9 AA9 SER A 112 ALA A 137 1 26 HELIX 10 AB1 SER A 145 ASN A 159 1 15 HELIX 11 AB2 SER A 164 GLY A 182 1 19 HELIX 12 AB3 SER A 186 GLY A 200 1 15 CRYST1 60.510 60.510 41.320 90.00 90.00 120.00 P 31 3 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 0.016526 0.009541 0.000000 0.00000 SCALE2 0.000000 0.019083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024201 0.00000 TER 1504 GLY A 200 HETATM 1505 O HOH A 301 6.199 55.145 6.784 1.00 40.02 O HETATM 1506 O HOH A 302 31.491 39.336 9.767 1.00 46.39 O HETATM 1507 O HOH A 303 11.277 28.643 10.319 1.00 38.29 O HETATM 1508 O HOH A 304 15.826 51.258 31.340 1.00 51.48 O HETATM 1509 O HOH A 305 4.368 54.978 19.828 1.00 29.51 O HETATM 1510 O HOH A 306 29.716 58.933 15.622 1.00 32.60 O HETATM 1511 O HOH A 307 21.793 38.470 2.385 1.00 43.31 O HETATM 1512 O HOH A 308 31.600 50.579 19.959 1.00 30.09 O HETATM 1513 O HOH A 309 17.464 34.689 7.068 1.00 35.23 O HETATM 1514 O HOH A 310 3.867 49.148 18.696 1.00 25.19 O HETATM 1515 O HOH A 311 12.585 50.645 3.918 1.00 31.29 O HETATM 1516 O HOH A 312 5.411 47.581 25.208 1.00 32.38 O HETATM 1517 O HOH A 313 12.264 33.592 -2.359 1.00 26.33 O HETATM 1518 O HOH A 314 5.034 30.386 7.800 1.00 30.52 O HETATM 1519 O HOH A 315 27.019 47.815 25.375 1.00 22.58 O HETATM 1520 O HOH A 316 16.211 21.536 8.264 1.00 31.74 O HETATM 1521 O HOH A 317 24.207 38.735 22.514 1.00 25.55 O HETATM 1522 O HOH A 318 18.093 52.890 8.825 1.00 24.83 O HETATM 1523 O HOH A 319 15.081 34.442 35.843 1.00 39.48 O HETATM 1524 O HOH A 320 20.362 40.890 -0.559 1.00 36.85 O HETATM 1525 O HOH A 321 18.591 43.249 33.724 1.00 42.97 O HETATM 1526 O HOH A 322 20.024 52.092 10.243 1.00 22.51 O HETATM 1527 O HOH A 323 31.319 45.351 19.887 1.00 21.52 O HETATM 1528 O HOH A 324 32.993 45.027 10.594 1.00 33.14 O HETATM 1529 O HOH A 325 13.066 48.340 2.623 1.00 25.73 O HETATM 1530 O HOH A 326 18.499 31.652 1.268 1.00 30.02 O HETATM 1531 O HOH A 327 38.175 31.704 13.740 1.00 41.31 O HETATM 1532 O HOH A 328 16.158 37.052 6.725 1.00 34.61 O HETATM 1533 O HOH A 329 3.343 35.885 4.382 1.00 44.98 O HETATM 1534 O HOH A 330 13.098 43.104 14.809 1.00 33.81 O HETATM 1535 O HOH A 331 11.168 66.522 11.961 1.00 51.96 O HETATM 1536 O HOH A 332 13.373 35.231 -3.480 1.00 52.50 O HETATM 1537 O HOH A 333 29.487 56.973 13.799 1.00 22.94 O HETATM 1538 O HOH A 334 16.890 25.875 -2.060 1.00 43.42 O HETATM 1539 O HOH A 335 16.817 26.013 35.519 1.00 52.24 O HETATM 1540 O HOH A 336 18.618 19.625 18.130 1.00 53.41 O HETATM 1541 O HOH A 337 27.694 55.101 21.753 1.00 41.07 O HETATM 1542 O HOH A 338 6.083 32.307 3.223 1.00 47.83 O HETATM 1543 O HOH A 339 10.183 39.640 13.821 1.00 44.45 O MASTER 249 0 0 12 0 0 0 6 1542 1 0 16 END