HEADER LYASE 26-DEC-24 9HVB TITLE HIGH-EFFICIENCY KEMP ELIMINASES BY COMPLETE COMPUTATIONAL DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: KEMP ELIMINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MONOMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR D.LISTOV,O.DYM,E.VOS,G.HOFFKA,A.BERG,S.ROGOTNER,S.CAROLINE, AUTHOR 2 L.KAMERLIN,S.J.FLEISHMAN REVDAT 4 13-AUG-25 9HVB 1 JRNL REVDAT 3 02-JUL-25 9HVB 1 JRNL REVDAT 2 25-JUN-25 9HVB 1 JRNL REVDAT 1 11-JUN-25 9HVB 0 JRNL AUTH D.LISTOV,E.VOS,G.HOFFKA,S.Y.HOCH,A.BERG,S.HAMER-ROGOTNER, JRNL AUTH 2 O.DYM,S.C.L.KAMERLIN,S.J.FLEISHMAN JRNL TITL COMPLETE COMPUTATIONAL DESIGN OF HIGH-EFFICIENCY KEMP JRNL TITL 2 ELIMINATION ENZYMES. JRNL REF NATURE V. 643 1421 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40533551 JRNL DOI 10.1038/S41586-025-09136-2 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2_3472: ???) 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) : 25.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15395 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 715 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 25.2200 - 3.4179 1.00 3008 135 0.1773 0.2387 REMARK 3 2 3.4179 - 2.7139 1.00 2909 168 0.2034 0.2245 REMARK 3 3 2.7139 - 2.3711 1.00 2923 130 0.2055 0.2417 REMARK 3 4 2.3711 - 2.1545 1.00 2932 144 0.1926 0.2628 REMARK 3 5 2.1545 - 2.0001 1.00 2908 138 0.2003 0.2781 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 24.410 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 : 0.007 1758 REMARK 3 ANGLE : 0.751 2391 REMARK 3 CHIRALITY : 0.056 288 REMARK 3 PLANARITY : 0.005 308 REMARK 3 DIHEDRAL : 2.453 1069 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 9HVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292144300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.34 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15405 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : 0.11360 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7300 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.03 REMARK 200 R MERGE FOR SHELL (I) : 0.50740 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.030 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 (%): 38.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M LITHIUM SULFATE MONOHYDRATE, REMARK 280 0.1 M CITRIC ACID (PH 3.5), AND 18% POLYETHYLENE GLYCOL (PEG) REMARK 280 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 13.49433 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 26.98867 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 20.24150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.73583 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 6.74717 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: 370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 LEU A 56 REMARK 465 ARG A 57 REMARK 465 LYS A 58 REMARK 465 SER A 59 REMARK 465 PRO A 60 REMARK 465 SER A 61 REMARK 465 GLY A 62 REMARK 465 LEU A 63 REMARK 465 ASP A 64 REMARK 465 VAL A 65 REMARK 465 GLU A 66 REMARK 465 ARG A 67 REMARK 465 GLY A 218 REMARK 465 TYR A 219 REMARK 465 SER A 220 REMARK 465 THR A 221 REMARK 465 LYS A 222 REMARK 465 GLU A 223 REMARK 465 GLU A 224 REMARK 465 LEU A 225 REMARK 465 LYS A 226 REMARK 465 GLU A 239 REMARK 465 SER A 240 REMARK 465 LEU A 241 REMARK 465 MET A 242 REMARK 465 ARG A 243 REMARK 465 ALA A 244 REMARK 465 GLY A 256 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 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 78 CE NZ REMARK 470 HIS A 92 ND1 CD2 CE1 NE2 REMARK 470 GLU A 166 CD OE1 OE2 REMARK 470 GLU A 178 CD OE1 OE2 REMARK 470 GLN A 185 CD OE1 NE2 REMARK 470 ARG A 194 NE CZ NH1 NH2 REMARK 470 GLU A 198 CD OE1 OE2 REMARK 470 MET A 228 CG SD CE REMARK 470 ARG A 229 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 249 CD CE NZ 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 SER A 2 110.70 -167.12 REMARK 500 GLN A 129 22.21 83.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 9HVB A 1 256 PDB 9HVB 9HVB 1 256 SEQRES 1 A 256 PRO SER ALA LEU ASP ALA ILE VAL ALA ASP VAL ARG GLU SEQRES 2 A 256 ASP VAL ALA ALA ARG GLU ALA VAL VAL PRO PHE ASP GLU SEQRES 3 A 256 ILE LYS GLU ARG ALA ALA ARG ALA PRO PRO PRO ARG ASP SEQRES 4 A 256 VAL LEU ALA ALA LEU ARG ALA PRO GLY VAL GLY ILE ILE SEQRES 5 A 256 ALA VAL TYR LEU ARG LYS SER PRO SER GLY LEU ASP VAL SEQRES 6 A 256 GLU ARG ASP PRO ILE GLU TYR ALA LYS THR ALA GLU LYS SEQRES 7 A 256 TYR ALA VAL ALA LEU VAL VAL ILE THR ASP GLU LYS TYR SEQRES 8 A 256 HIS ASN GLY SER TYR GLU ASP LEU GLU LYS ILE ARG SER SEQRES 9 A 256 ALA VAL ASP ILE PRO VAL ILE CYS PHE ASP PHE ILE VAL SEQRES 10 A 256 ASP PRO TYR GLN ILE TYR LEU ALA ARG ALA TYR GLN ALA SEQRES 11 A 256 ASP ALA ILE VAL LEU ILE LEU SER VAL LEU ASP ASP GLU SEQRES 12 A 256 GLN TYR ARG GLN LEU ALA ALA VAL ALA HIS SER LEU ASN SEQRES 13 A 256 MET GLY VAL ILE VAL ASP VAL HIS THR GLU GLU GLU LEU SEQRES 14 A 256 GLU ARG ALA LEU LYS ALA GLY ALA GLU ILE ILE GLY ILE SEQRES 15 A 256 VAL ASN GLN ASP LEU LYS THR PHE GLU VAL ASP ARG ASN SEQRES 16 A 256 THR ALA GLU ARG LEU GLY ARG LEU ALA ARG GLU ARG GLY SEQRES 17 A 256 PHE THR GLY VAL LEU LEU ALA ILE GLY GLY TYR SER THR SEQRES 18 A 256 LYS GLU GLU LEU LYS SER MET ARG GLY LEU PHE ASP ALA SEQRES 19 A 256 VAL VAL ILE GLY GLU SER LEU MET ARG ALA PRO ASP PRO SEQRES 20 A 256 GLU LYS ALA ILE ARG GLU LEU VAL GLY HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *101(H2 O) HELIX 1 AA1 SER A 2 ALA A 20 1 19 HELIX 2 AA2 PRO A 23 ARG A 33 1 11 HELIX 3 AA3 ASP A 39 ALA A 46 1 8 HELIX 4 AA4 PRO A 69 GLU A 77 1 9 HELIX 5 AA5 GLY A 94 VAL A 106 1 13 HELIX 6 AA6 ASP A 118 TYR A 128 1 11 HELIX 7 AA7 ASP A 141 LEU A 155 1 15 HELIX 8 AA8 THR A 165 GLY A 176 1 12 HELIX 9 AA9 ASN A 195 ARG A 207 1 13 HELIX 10 AB1 ASP A 246 VAL A 255 1 10 SHEET 1 AA1 9 GLY A 50 TYR A 55 0 SHEET 2 AA1 9 ALA A 82 ILE A 86 1 O VAL A 84 N ALA A 53 SHEET 3 AA1 9 VAL A 110 PHE A 113 1 O ILE A 111 N LEU A 83 SHEET 4 AA1 9 ALA A 132 ILE A 136 1 O ALA A 132 N CYS A 112 SHEET 5 AA1 9 GLY A 158 VAL A 163 1 O ILE A 160 N LEU A 135 SHEET 6 AA1 9 ILE A 179 VAL A 183 1 O GLY A 181 N VAL A 163 SHEET 7 AA1 9 VAL A 212 ILE A 216 1 O VAL A 212 N ILE A 180 SHEET 8 AA1 9 ALA A 234 ILE A 237 1 O VAL A 236 N ALA A 215 SHEET 9 AA1 9 GLY A 50 TYR A 55 1 N ILE A 52 O ILE A 237 CRYST1 98.541 98.541 40.483 90.00 90.00 120.00 P 61 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 0.010148 0.005859 0.000000 0.00000 SCALE2 0.000000 0.011718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024701 0.00000 CONECT 1728 1729 1730 1731 1732 CONECT 1729 1728 CONECT 1730 1728 CONECT 1731 1728 CONECT 1732 1728 CONECT 1733 1734 1735 1736 1737 CONECT 1734 1733 CONECT 1735 1733 CONECT 1736 1733 CONECT 1737 1733 MASTER 276 0 2 10 9 0 0 6 1837 1 10 20 END