HEADER DE NOVO PROTEIN 26-JAN-26 9U01 TITLE DE NOVO TIM BARREL WITH KEMP ELIMINASE ACTIVITY - KEMPTIM1 (APO) COMPND MOL_ID: 1; COMPND 2 MOLECULE: KEMPTIM1; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS KEMP ELIMINASE, DE NOVO, TIM BARREL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KRIEGEL,J.BECK,R.A.CHICA,B.HOCKER REVDAT 1 24-JUN-26 9U01 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. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2099 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 33.3400 - 3.0800 1.00 3753 149 0.1651 0.1542 REMARK 3 2 3.0800 - 2.4500 1.00 3600 143 0.1578 0.1937 REMARK 3 3 2.4500 - 2.1400 1.00 3564 142 0.1304 0.1664 REMARK 3 4 2.1400 - 1.9400 1.00 3537 140 0.1333 0.1750 REMARK 3 5 1.9400 - 1.8000 1.00 3513 140 0.1345 0.1489 REMARK 3 6 1.8000 - 1.7000 1.00 3530 140 0.1323 0.1864 REMARK 3 7 1.7000 - 1.6100 1.00 3503 139 0.1320 0.1470 REMARK 3 8 1.6100 - 1.5400 1.00 3489 139 0.1431 0.1861 REMARK 3 9 1.5400 - 1.4800 1.00 3472 138 0.1567 0.2038 REMARK 3 10 1.4800 - 1.4300 1.00 3495 139 0.1820 0.2360 REMARK 3 11 1.4300 - 1.3900 1.00 3484 139 0.2025 0.2279 REMARK 3 12 1.3900 - 1.3500 1.00 3476 138 0.2110 0.2364 REMARK 3 13 1.3500 - 1.3100 1.00 3467 138 0.2262 0.2727 REMARK 3 14 1.3100 - 1.2800 1.00 3484 138 0.2617 0.3262 REMARK 3 15 1.2800 - 1.2500 1.00 3451 137 0.2967 0.3263 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) : 0.141 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.834 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.50 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 : 0.011 1794 REMARK 3 ANGLE : 1.089 2435 REMARK 3 CHIRALITY : 0.083 282 REMARK 3 PLANARITY : 0.013 330 REMARK 3 DIHEDRAL : 13.865 687 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 9U01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1292153768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.9184 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 : 54927 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 33.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.28 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 (%): 40.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS REMARK 280 PH 5.5, 25% W/V PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 20.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.57000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.34500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.57000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.34500 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 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 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 -3 REMARK 465 GLY A -2 REMARK 465 TRP A 219 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 171 75.52 75.72 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 585 DISTANCE = 5.81 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9TZD RELATED DB: PDB DBREF 9U01 A -3 219 PDB 9U01 9U01 -3 219 SEQRES 1 A 223 SER GLY SER GLY GLU ILE ALA TYR ALA SER GLY ASP ALA SEQRES 2 A 223 ASP HIS LEU LEU ALA ALA ARG GLU ALA GLY ALA ASP ILE SEQRES 3 A 223 LEU ASP VAL VAL ASP VAL ASP PRO ALA ARG ALA LEU ALA SEQRES 4 A 223 GLN VAL ARG ARG LEU ARG ALA ALA GLY ALA ARG ARG ILE SEQRES 5 A 223 LEU TYR ALA SER LEU ARG VAL ASP ASP LEU LEU ALA ALA SEQRES 6 A 223 LEU GLU ALA GLY ALA ASP ILE LEU ALA VAL PRO ASP LEU SEQRES 7 A 223 ASP HIS ASP ALA ALA LEU ALA GLN ILE ARG ALA LEU LYS SEQRES 8 A 223 ALA ALA GLY ALA ARG GLU ILE ALA TYR GLY SER PRO ASP SEQRES 9 A 223 ALA ASP HIS LEU LEU GLU ALA ARG GLU ALA GLY ALA ASP SEQRES 10 A 223 ILE LEU GLY VAL ALA ALA ASP THR PRO ALA VAL ARG GLU SEQRES 11 A 223 LEU TRP LEU ARG ASN LEU ARG GLN VAL PHE SER GLU GLU SEQRES 12 A 223 GLU ALA ARG GLU ILE LEU ASP ARG ARG ILE HIS LEU PRO SEQRES 13 A 223 ASP PRO ALA THR ALA ILE GLU GLN VAL ARG ARG LEU ARG SEQRES 14 A 223 ALA ALA GLY ALA LYS ARG ILE MET PHE ALA SER ASP ASP SEQRES 15 A 223 VAL ASP HIS LEU ALA ALA ALA LYS ARG ALA GLY ALA ASP SEQRES 16 A 223 ILE LEU LEU VAL ALA GLU ALA GLY GLY SER ALA GLU ALA SEQRES 17 A 223 ARG ALA ALA ALA LEU ALA GLN VAL ARG ARG LEU LYS ALA SEQRES 18 A 223 LEU TRP HET EDO A 300 10 HET EDO A 301 10 HET EDO A 302 10 HET EDO A 303 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 HOH *185(H2 O) HELIX 1 AA1 ASP A 8 ALA A 18 1 11 HELIX 2 AA2 ASP A 29 ALA A 43 1 15 HELIX 3 AA3 ARG A 54 GLY A 65 1 12 HELIX 4 AA4 ASP A 75 ALA A 89 1 15 HELIX 5 AA5 ASP A 100 ALA A 110 1 11 HELIX 6 AA6 THR A 121 ARG A 133 1 13 HELIX 7 AA7 SER A 137 ARG A 148 1 12 HELIX 8 AA8 ASP A 153 GLY A 168 1 16 HELIX 9 AA9 ASP A 178 GLY A 189 1 12 HELIX 10 AB1 SER A 201 LEU A 218 1 18 SHEET 1 AA1 9 GLU A 1 SER A 6 0 SHEET 2 AA1 9 ILE A 22 VAL A 25 1 O ASP A 24 N TYR A 4 SHEET 3 AA1 9 ILE A 48 ALA A 51 1 O LEU A 49 N LEU A 23 SHEET 4 AA1 9 ILE A 68 PRO A 72 1 O ALA A 70 N TYR A 50 SHEET 5 AA1 9 ILE A 94 GLY A 97 1 O ALA A 95 N LEU A 69 SHEET 6 AA1 9 ILE A 114 ALA A 118 1 O GLY A 116 N TYR A 96 SHEET 7 AA1 9 ILE A 172 ALA A 175 1 O MET A 173 N VAL A 117 SHEET 8 AA1 9 ILE A 192 ALA A 196 1 O LEU A 194 N PHE A 174 SHEET 9 AA1 9 GLU A 1 SER A 6 1 N ALA A 3 O LEU A 193 CRYST1 41.170 66.690 71.140 90.00 90.00 90.00 P 21 21 21 4 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 0.024290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014057 0.00000 CONECT 3578 3579 3580 3582 3583 CONECT 3579 3578 3584 CONECT 3580 3578 3581 3585 3586 CONECT 3581 3580 3587 CONECT 3582 3578 CONECT 3583 3578 CONECT 3584 3579 CONECT 3585 3580 CONECT 3586 3580 CONECT 3587 3581 CONECT 3588 3589 3590 3592 3593 CONECT 3589 3588 3594 CONECT 3590 3588 3591 3595 3596 CONECT 3591 3590 3597 CONECT 3592 3588 CONECT 3593 3588 CONECT 3594 3589 CONECT 3595 3590 CONECT 3596 3590 CONECT 3597 3591 CONECT 3598 3599 3600 3602 3603 CONECT 3599 3598 3604 CONECT 3600 3598 3601 3605 3606 CONECT 3601 3600 3607 CONECT 3602 3598 CONECT 3603 3598 CONECT 3604 3599 CONECT 3605 3600 CONECT 3606 3600 CONECT 3607 3601 CONECT 3608 3609 3610 3612 3613 CONECT 3609 3608 3614 CONECT 3610 3608 3611 3615 3616 CONECT 3611 3610 3617 CONECT 3612 3608 CONECT 3613 3608 CONECT 3614 3609 CONECT 3615 3610 CONECT 3616 3610 CONECT 3617 3611 MASTER 251 0 4 10 9 0 0 6 1841 1 40 18 END