HEADER BIOSYNTHETIC PROTEIN 15-NOV-22 8BP0 TITLE CRYSTAL STRUCTURE OF BHMEHIS1.8, AN ENGINEERED ENZYME FOR THE MORITA- TITLE 2 BAYLIS-HILLMAN REACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BHMEHIS1.8; 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 MORITA-BAYLIS-HILLMANASE, NON-CANONICAL AMINO ACID, METHYLHISTIDINE, KEYWDS 2 DE NOVO ENZYME, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.J.HARDY REVDAT 3 13-MAR-24 8BP0 1 JRNL REVDAT 2 06-MAR-24 8BP0 1 JRNL REVDAT 1 28-FEB-24 8BP0 0 JRNL AUTH A.E.HUTTON,J.FOSTER,R.CRAWSHAW,F.J.HARDY,L.O.JOHANNISSEN, JRNL AUTH 2 T.M.LISTER,E.F.GERARD,Z.BIRCH-PRICE,R.OBEXER,S.HAY,A.P.GREEN JRNL TITL A NON-CANONICAL NUCLEOPHILE UNLOCKS A NEW MECHANISTIC JRNL TITL 2 PATHWAY IN A DESIGNED ENZYME. JRNL REF NAT COMMUN V. 15 1956 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38438341 JRNL DOI 10.1038/S41467-024-46123-Z REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.CROSSLEY,R.CRAWSHAW,F.HARDY,L.JOHANNISSEN,T.LISTER, REMARK 1 AUTH 2 E.GERARD,Z.BIRCH-PRICE,R.OBEXER,S.HAY,A.GREEN REMARK 1 TITL A NON-CANONICAL NUCLEOPHILE UNLOCKS A NEW MECHANISTIC REMARK 1 TITL 2 PATHWAY IN A DESIGNED ENZYME REMARK 1 REF RES SQ 2023 REMARK 1 REFN ESSN 2693-5015 REMARK 1 DOI 10.21203/RS.3.RS-2922796/V1 REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7412 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 400 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 38.1500 - 3.7800 1.00 2451 131 0.1740 0.2172 REMARK 3 2 3.7800 - 3.0000 1.00 2294 135 0.1909 0.2359 REMARK 3 3 3.0000 - 2.6210 1.00 2267 134 0.2339 0.3088 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) : 0.315 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.87 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 1925 REMARK 3 ANGLE : 0.449 2588 REMARK 3 CHIRALITY : 0.039 274 REMARK 3 PLANARITY : 0.004 331 REMARK 3 DIHEDRAL : 6.787 269 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 8BP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126499. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-22 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7422 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.621 REMARK 200 RESOLUTION RANGE LOW (A) : 38.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 26.10 REMARK 200 R MERGE (I) : 0.25350 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 25.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: 7O1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M BIS-TRIS, PH = 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 17.72850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.29150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.21550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.29150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.72850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.21550 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 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 GLY A 231 REMARK 465 GLN A 232 REMARK 465 GLY A 233 REMARK 465 SER A 234 REMARK 465 LEU A 235 REMARK 465 GLU A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 8 OH TYR A 177 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 9 153.95 70.70 REMARK 500 LEU A 13 -33.81 -133.73 REMARK 500 LYS A 184 18.32 -140.19 REMARK 500 SER A 189 41.98 -90.43 REMARK 500 LYS A 211 57.13 -112.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 8BP0 A 1 242 PDB 8BP0 8BP0 1 242 SEQRES 1 A 242 MET ILE ARG ALA VAL PHE PHE ASP SER LEU GLY THR LEU SEQRES 2 A 242 ILE SER VAL GLU GLY ALA TYR LYS ILE MHS VAL LYS GLU SEQRES 3 A 242 MET GLU GLU VAL LEU GLY ASP TYR PRO LEU ASN PRO ARG SEQRES 4 A 242 THR LEU TRP ASP GLU PHE ASP LYS LEU PHE LYS GLU ALA SEQRES 5 A 242 PHE SER ASN TYR ALA GLY LYS PRO TYR ARG PRO ALA ARG SEQRES 6 A 242 PHE ILE LEU GLU GLU VAL MET ARG LYS LEU ALA GLU LYS SEQRES 7 A 242 TYR GLY PHE LYS TYR PRO GLY ASN LEU GLN GLU ILE GLY SEQRES 8 A 242 VAL ARG MET ALA ARG ARG TYR GLY GLY LEU TYR PRO GLU SEQRES 9 A 242 VAL VAL GLU VAL LEU LYS SER LEU LYS GLY LYS TYR HIS SEQRES 10 A 242 VAL GLY VAL ILE LEU ASN TRP ASP THR GLU ASN ALA THR SEQRES 11 A 242 ALA PHE LEU ASP ALA LEU GLY ILE LYS ASP LEU PHE ASP SEQRES 12 A 242 SER ILE THR THR SER GLU GLU ALA GLY PHE ALA TYR PRO SEQRES 13 A 242 HIS PRO ARG ILE LEU GLU LEU ALA LEU LYS LYS ALA GLY SEQRES 14 A 242 VAL LYS GLY GLU LYS ALA VAL TYR VAL GLY ASP ASN PRO SEQRES 15 A 242 VAL LYS ASP ALA GLY GLY SER LYS ASN LEU GLY MET THR SEQRES 16 A 242 SER ILE LEU LEU ASP ARG LYS GLY GLU LYS ARG GLU PHE SEQRES 17 A 242 TRP ASP LYS ALA ASP PHE ARG VAL SER ASP LEU ARG GLU SEQRES 18 A 242 VAL ILE LYS ILE VAL ASP GLU LEU ASN GLY GLN GLY SER SEQRES 19 A 242 LEU GLU HIS HIS HIS HIS HIS HIS HET MHS A 23 19 HET PGE A 301 24 HET EDO A 302 10 HET EDO A 303 10 HETNAM MHS N1-METHYLATED HISTIDINE HETNAM PGE TRIETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MHS C7 H11 N3 O2 FORMUL 2 PGE C6 H14 O4 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *77(H2 O) HELIX 1 AA1 LEU A 10 LEU A 13 5 4 HELIX 2 AA2 SER A 15 GLY A 32 1 18 HELIX 3 AA3 ASN A 37 ASN A 55 1 19 HELIX 4 AA4 PRO A 63 GLY A 80 1 18 HELIX 5 AA5 ASN A 86 GLY A 99 1 14 HELIX 6 AA6 GLU A 104 TYR A 116 1 13 HELIX 7 AA7 ASP A 125 GLY A 137 1 13 HELIX 8 AA8 ILE A 138 PHE A 142 5 5 HELIX 9 AA9 SER A 148 GLY A 152 1 5 HELIX 10 AB1 HIS A 157 GLY A 169 1 13 HELIX 11 AB2 LYS A 171 GLU A 173 5 3 HELIX 12 AB3 LYS A 205 TRP A 209 5 5 HELIX 13 AB4 ARG A 220 LEU A 229 1 10 SHEET 1 AA1 6 SER A 144 THR A 147 0 SHEET 2 AA1 6 HIS A 117 LEU A 122 1 N VAL A 120 O THR A 146 SHEET 3 AA1 6 ALA A 4 ASP A 8 1 N VAL A 5 O HIS A 117 SHEET 4 AA1 6 ALA A 175 GLY A 179 1 O VAL A 178 N PHE A 6 SHEET 5 AA1 6 THR A 195 LEU A 199 1 O ILE A 197 N TYR A 177 SHEET 6 AA1 6 PHE A 214 VAL A 216 1 O PHE A 214 N LEU A 198 LINK C ILE A 22 N MHS A 23 1555 1555 1.33 LINK C MHS A 23 N VAL A 24 1555 1555 1.33 CISPEP 1 TYR A 155 PRO A 156 0 -4.60 CRYST1 35.457 42.431 152.583 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 0.028203 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006554 0.00000