HEADER DE NOVO PROTEIN 17-APR-26 12TD TITLE STRUCTURE OF DE NOVO DESIGNED SALEN-BINDING ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED SALEN-BINDING ENZYME; COMPND 3 CHAIN: A, B; 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 ENZYME, SALEN-BINDING PROTEIN, HELICAL BUNDLE, DE NOVO DESIGN, DE KEYWDS 2 NOVO ENZYME, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.BAKANAS,M.HORST,W.F.DEGRADO REVDAT 1 29-APR-26 12TD 0 JRNL AUTH I.BAKANAS,M.HORST,W.F.DEGRADO JRNL TITL DE NOVO DESIGN OF CATALYTICALLY ACTIVE SALEN-BINDING JRNL TITL 2 PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 2.0_5848 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18937 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) : 0.214 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1895 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 57.4100 - 4.8000 1.00 1295 145 0.2201 0.2462 REMARK 3 2 4.7900 - 3.8100 1.00 1260 140 0.1717 0.2137 REMARK 3 3 3.8100 - 3.3300 1.00 1220 135 0.1780 0.2134 REMARK 3 4 3.3300 - 3.0200 1.00 1226 137 0.2061 0.2645 REMARK 3 5 3.0200 - 2.8100 1.00 1221 136 0.2209 0.3115 REMARK 3 6 2.8000 - 2.6400 1.00 1209 134 0.2268 0.2583 REMARK 3 7 2.6400 - 2.5100 1.00 1203 134 0.2123 0.2701 REMARK 3 8 2.5100 - 2.4000 1.00 1203 134 0.2100 0.2334 REMARK 3 9 2.4000 - 2.3100 1.00 1218 135 0.2165 0.2718 REMARK 3 10 2.3100 - 2.2300 1.00 1191 132 0.2957 0.3923 REMARK 3 11 2.2300 - 2.1600 1.00 1207 135 0.2666 0.3324 REMARK 3 12 2.1600 - 2.1000 1.00 1212 135 0.2937 0.3139 REMARK 3 13 2.0900 - 2.0400 0.99 1185 131 0.3426 0.3802 REMARK 3 14 2.0400 - 1.9900 1.00 1192 132 0.3435 0.3946 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) : 0.294 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.29 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 : 0.005 2276 REMARK 3 ANGLE : 0.674 3073 REMARK 3 CHIRALITY : 0.035 353 REMARK 3 PLANARITY : 0.008 401 REMARK 3 DIHEDRAL : 23.194 841 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 12TD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000307235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11582 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18978 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 81.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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 (%): 40.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.75 M HEPES PH 7.5, 0.7 M SODIUM REMARK 280 CITRATE, 0.075 M SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 40.77250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.77250 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 1.000000 0.000000 0.000000 38.39600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.22450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.39600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.22450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.77250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.39600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.22450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.77250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.39600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.22450 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -40.77250 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 SER A -1 REMARK 465 GLY A 0 REMARK 465 SER B -1 REMARK 465 GLY B 0 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 THR A 65 99.02 -54.41 REMARK 500 PHE A 69 47.69 -82.56 REMARK 500 ARG A 70 -58.98 -19.85 REMARK 500 TYR B 68 -67.57 -97.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 12TD A -1 144 PDB 12TD 12TD -1 144 DBREF 12TD B -1 144 PDB 12TD 12TD -1 144 SEQRES 1 A 146 SER GLY GLY GLU LEU ALA ALA ILE ILE ALA LYS ILE LYS SEQRES 2 A 146 GLU THR GLY ALA LYS ILE LEU GLU LEU PHE THR ARG ALA SEQRES 3 A 146 LEU ASP THR LEU VAL ASP GLY ASP GLU ALA GLU PHE ARG SEQRES 4 A 146 LYS ILE LEU GLU GLU LEU THR LYS LEU VAL LYS GLU HIS SEQRES 5 A 146 PHE ALA LEU VAL SER GLU ALA ILE ALA ALA GLY ALA PRO SEQRES 6 A 146 VAL THR PRO GLY TYR PHE ARG GLY VAL GLU LEU VAL ALA SEQRES 7 A 146 LEU PHE GLU ALA PHE VAL LYS ALA TYR GLU ASP GLY ASP SEQRES 8 A 146 GLU GLY ALA PHE LEU ARG LEU GLY ALA GLN LEU ALA VAL SEQRES 9 A 146 LEU ALA LEU ALA GLY GLY LEU PRO ARG GLU VAL ALA ARG SEQRES 10 A 146 ARG PHE LEU GLU TRP ALA LEU GLU ARG LEU ARG ARG LEU SEQRES 11 A 146 GLY ASP GLU GLU GLY ALA ALA GLU VAL GLN ARG TYR LEU SEQRES 12 A 146 ASP THR LEU SEQRES 1 B 146 SER GLY GLY GLU LEU ALA ALA ILE ILE ALA LYS ILE LYS SEQRES 2 B 146 GLU THR GLY ALA LYS ILE LEU GLU LEU PHE THR ARG ALA SEQRES 3 B 146 LEU ASP THR LEU VAL ASP GLY ASP GLU ALA GLU PHE ARG SEQRES 4 B 146 LYS ILE LEU GLU GLU LEU THR LYS LEU VAL LYS GLU HIS SEQRES 5 B 146 PHE ALA LEU VAL SER GLU ALA ILE ALA ALA GLY ALA PRO SEQRES 6 B 146 VAL THR PRO GLY TYR PHE ARG GLY VAL GLU LEU VAL ALA SEQRES 7 B 146 LEU PHE GLU ALA PHE VAL LYS ALA TYR GLU ASP GLY ASP SEQRES 8 B 146 GLU GLY ALA PHE LEU ARG LEU GLY ALA GLN LEU ALA VAL SEQRES 9 B 146 LEU ALA LEU ALA GLY GLY LEU PRO ARG GLU VAL ALA ARG SEQRES 10 B 146 ARG PHE LEU GLU TRP ALA LEU GLU ARG LEU ARG ARG LEU SEQRES 11 B 146 GLY ASP GLU GLU GLY ALA ALA GLU VAL GLN ARG TYR LEU SEQRES 12 B 146 ASP THR LEU FORMUL 3 HOH *82(H2 O) HELIX 1 AA1 GLU A 2 ASP A 30 1 29 HELIX 2 AA2 ASP A 32 GLY A 61 1 30 HELIX 3 AA3 GLU A 73 ASP A 87 1 15 HELIX 4 AA4 ASP A 89 LEU A 105 1 17 HELIX 5 AA5 ALA A 106 GLY A 108 5 3 HELIX 6 AA6 PRO A 110 LEU A 128 1 19 HELIX 7 AA7 ASP A 130 LEU A 144 1 15 HELIX 8 AA8 GLU B 2 GLY B 31 1 30 HELIX 9 AA9 ASP B 32 GLY B 61 1 30 HELIX 10 AB1 TYR B 68 ASP B 87 1 20 HELIX 11 AB2 ASP B 89 ALA B 106 1 18 HELIX 12 AB3 PRO B 110 GLY B 129 1 20 HELIX 13 AB4 ASP B 130 LEU B 144 1 15 CRYST1 76.792 86.449 81.545 90.00 90.00 90.00 C 2 2 21 16 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 0.013022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012263 0.00000 MASTER 257 0 0 13 0 0 0 6 2314 2 0 24 END