HEADER DE NOVO PROTEIN 20-MAR-25 9QKX TITLE DE NOVO TIM BARREL WITH KEMP ELIMINASE ACTIVITY - KEMPTIM4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: DE NOVO; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS KEMP ELIMINASE, DE NOVO, TIM BARREL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.BECK,R.A.CHICA,B.HOCKER REVDAT 1 24-JUN-26 9QKX 0 JRNL AUTH J.BECK,B.J.SMITH,M.KRIEGEL,N.ZARIFI,E.FREUND,A.G.HARSHA, JRNL AUTH 2 J.HARTMANN,R.A.CHICA,B.HOCKER JRNL TITL CUSTOMIZING THE STRUCTURE OF MINIMAL TIM BARRELS TO CRAFT JRNL TITL 2 EFFICIENT DE NOVO ENZYMES JRNL REF NAT.CHEM.BIOL. 2026 JRNL REFN ESSN 1552-4469 JRNL DOI 10.1038/S41589-026-02250-W REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 11454 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 574 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 47.5900 - 3.6500 0.99 2864 151 0.2112 0.2460 REMARK 3 2 3.6500 - 2.9000 0.99 2717 144 0.2508 0.3231 REMARK 3 3 2.9000 - 2.5300 0.98 2668 139 0.3209 0.3688 REMARK 3 4 2.5300 - 2.3000 0.98 2631 140 0.3530 0.3799 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) : 0.414 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.322 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.19 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 1693 REMARK 3 ANGLE : 0.297 2277 REMARK 3 CHIRALITY : 0.035 270 REMARK 3 PLANARITY : 0.002 292 REMARK 3 DIHEDRAL : 8.201 622 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 9QKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292146457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11469 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 47.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : 0.46880 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.87300 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 (%): 53.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 40.23000 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 80.46000 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 80.46000 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 40.23000 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 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 157 42.33 -83.12 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 448 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 449 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 450 DISTANCE = 7.52 ANGSTROMS REMARK 525 HOH A 451 DISTANCE = 8.50 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 11.76 ANGSTROMS DBREF 9QKX A 1 221 PDB 9QKX 9QKX 1 221 SEQRES 1 A 221 SER ARG ILE ALA TYR MET ALA LEU ALA SER ASP LEU ASP SEQRES 2 A 221 SER LEU VAL GLU ALA LEU LYS LEU GLY ALA ASP ILE LEU SEQRES 3 A 221 MET VAL ALA LEU MET ALA ASP ALA ALA ALA VAL ARG ALA SEQRES 4 A 221 MET ALA GLU GLY LEU HIS ALA ASN GLY ASP PRO ARG SER SEQRES 5 A 221 VAL ALA GLU LEU GLU ALA LEU LEU ARG PRO THR ASP LEU SEQRES 6 A 221 ASP ASP ALA LEU ALA ALA VAL ARG GLU LEU LYS ALA LEU SEQRES 7 A 221 GLY ALA LYS GLU ILE ALA PHE MET SER HIS ASP VAL ASP SEQRES 8 A 221 HIS LEU ILE ARG ALA MET GLU ALA GLY ALA ASP ILE LEU SEQRES 9 A 221 MET VAL LEU GLU SER SER ALA THR SER VAL GLU ALA ALA SEQRES 10 A 221 LEU ALA GLN VAL ARG ARG LEU LYS ALA ALA GLY ALA LYS SEQRES 11 A 221 ARG ILE SER PHE GLY SER GLY ASP VAL ALA HIS LEU LYS SEQRES 12 A 221 ALA ALA MET GLU ALA GLY ALA ASP ILE LEU ASP VAL LEU SEQRES 13 A 221 GLU ARG HIS GLY LEU ASP VAL ALA LEU ALA GLN ILE ARG SEQRES 14 A 221 GLU LEU LYS ALA ALA GLY ALA LYS GLU ILE ALA PHE ALA SEQRES 15 A 221 SER LEU ASP PRO ASP HIS LEU LEU ARG ALA ARG GLU GLU SEQRES 16 A 221 GLY ALA ASP ILE LEU VAL VAL PHE GLY ALA THR ASP PRO SEQRES 17 A 221 ALA ARG ALA LEU ALA THR VAL ARG TYR LEU ARG ALA TRP HET GOL A 301 6 HET GOL A 302 6 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 7(C3 H8 O3) FORMUL 9 HOH *52(H2 O) HELIX 1 AA1 ASP A 11 GLY A 22 1 12 HELIX 2 AA2 ASP A 33 ASN A 47 1 15 HELIX 3 AA3 SER A 52 LEU A 60 1 9 HELIX 4 AA4 ASP A 64 LEU A 78 1 15 HELIX 5 AA5 ASP A 89 GLY A 100 1 12 HELIX 6 AA6 SER A 113 ALA A 127 1 15 HELIX 7 AA7 ASP A 138 GLY A 149 1 12 HELIX 8 AA8 GLY A 160 GLY A 175 1 16 HELIX 9 AA9 ASP A 185 GLY A 196 1 12 HELIX 10 AB1 ASP A 207 ARG A 219 1 13 SHEET 1 AA1 9 ARG A 2 LEU A 8 0 SHEET 2 AA1 9 ILE A 25 ALA A 29 1 O ALA A 29 N ALA A 7 SHEET 3 AA1 9 ILE A 83 MET A 86 1 O ALA A 84 N VAL A 28 SHEET 4 AA1 9 ILE A 103 LEU A 107 1 O ILE A 103 N PHE A 85 SHEET 5 AA1 9 ILE A 132 SER A 136 1 O SER A 133 N VAL A 106 SHEET 6 AA1 9 ILE A 152 LEU A 156 1 O ASP A 154 N PHE A 134 SHEET 7 AA1 9 ILE A 179 SER A 183 1 O ALA A 180 N LEU A 153 SHEET 8 AA1 9 ILE A 199 PHE A 203 1 O VAL A 201 N PHE A 181 SHEET 9 AA1 9 ARG A 2 LEU A 8 1 N ALA A 4 O LEU A 200 CRYST1 59.800 59.800 120.690 90.00 90.00 120.00 P 31 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 0.016722 0.009655 0.000000 0.00000 SCALE2 0.000000 0.019309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008286 0.00000 CONECT 1642 1643 1644 CONECT 1643 1642 CONECT 1644 1642 1645 1646 CONECT 1645 1644 CONECT 1646 1644 1647 CONECT 1647 1646 CONECT 1648 1649 1650 CONECT 1649 1648 CONECT 1650 1648 1651 1652 CONECT 1651 1650 CONECT 1652 1650 1653 CONECT 1653 1652 CONECT 1654 1655 1656 CONECT 1655 1654 CONECT 1656 1654 1657 1658 CONECT 1657 1656 CONECT 1658 1656 1659 CONECT 1659 1658 CONECT 1660 1661 1662 CONECT 1661 1660 CONECT 1662 1660 1663 1664 CONECT 1663 1662 CONECT 1664 1662 1665 CONECT 1665 1664 CONECT 1666 1667 1668 CONECT 1667 1666 CONECT 1668 1666 1669 1670 CONECT 1669 1668 CONECT 1670 1668 1671 CONECT 1671 1670 CONECT 1672 1673 1674 CONECT 1673 1672 CONECT 1674 1672 1675 1676 CONECT 1675 1674 CONECT 1676 1674 1677 CONECT 1677 1676 CONECT 1678 1679 1680 CONECT 1679 1678 CONECT 1680 1678 1681 1682 CONECT 1681 1680 CONECT 1682 1680 1683 CONECT 1683 1682 MASTER 233 0 7 10 9 0 0 6 1726 1 42 17 END