HEADER BIOSYNTHETIC PROTEIN 29-MAR-21 7O1D TITLE A DE NOVO ENZYME FOR THE MORITA-BAYLIS-HILLMAN REACTION BH32.7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BH32.7 PROTEIN; 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 DE NOVO ENZYME, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.W.LEVY REVDAT 4 01-MAY-24 7O1D 1 REMARK REVDAT 3 16-MAR-22 7O1D 1 JRNL REVDAT 2 02-FEB-22 7O1D 1 JRNL REMARK REVDAT 1 03-NOV-21 7O1D 0 JRNL AUTH R.CRAWSHAW,A.E.CROSSLEY,L.JOHANNISSEN,A.J.BURKE,S.HAY, JRNL AUTH 2 C.LEVY,D.BAKER,S.L.LOVELOCK,A.P.GREEN JRNL TITL ENGINEERING AN EFFICIENT AND ENANTIOSELECTIVE ENZYME FOR THE JRNL TITL 2 MORITA-BAYLIS-HILLMAN REACTION. JRNL REF NAT.CHEM. V. 14 313 2022 JRNL REFN ESSN 1755-4349 JRNL PMID 34916595 JRNL DOI 10.1038/S41557-021-00833-9 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20803 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1067 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 45.1200 - 3.6000 0.97 2482 124 0.1747 0.2114 REMARK 3 2 3.6000 - 2.8600 0.99 2471 140 0.2055 0.2637 REMARK 3 3 2.8600 - 2.5000 0.99 2484 133 0.2313 0.2923 REMARK 3 4 2.5000 - 2.2700 1.00 2473 139 0.2127 0.2860 REMARK 3 5 2.2700 - 2.1100 0.99 2465 137 0.2173 0.2579 REMARK 3 6 2.1100 - 1.9800 0.99 2469 123 0.2442 0.2751 REMARK 3 7 1.9800 - 1.8800 0.99 2475 130 0.2500 0.3063 REMARK 3 8 1.8800 - 1.8000 0.99 2417 141 0.2989 0.3562 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) : 0.251 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.623 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.94 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 : 0.004 1866 REMARK 3 ANGLE : 0.538 2513 REMARK 3 CHIRALITY : 0.043 275 REMARK 3 PLANARITY : 0.004 321 REMARK 3 DIHEDRAL : 14.125 714 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -14.1968 -12.2306 -11.2380 REMARK 3 T TENSOR REMARK 3 T11: 0.2496 T22: 0.2142 REMARK 3 T33: 0.2509 T12: 0.0327 REMARK 3 T13: 0.0064 T23: 0.0417 REMARK 3 L TENSOR REMARK 3 L11: 1.2576 L22: 1.3828 REMARK 3 L33: 1.3474 L12: 0.8197 REMARK 3 L13: 0.3799 L23: 0.6077 REMARK 3 S TENSOR REMARK 3 S11: 0.0235 S12: -0.1007 S13: -0.0612 REMARK 3 S21: 0.1454 S22: -0.0988 S23: -0.0114 REMARK 3 S31: 0.1529 S32: 0.0405 S33: 0.0003 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 7O1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.03660 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.270 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: INHOUSE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BICINE PH 9.3 25% PEG SMEAR REMARK 280 MEDIUM BCS SCREEN CONDITION B6, PH 7, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.81500 REMARK 290 SMTRY3 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 VAL A 183 REMARK 465 LYS A 184 REMARK 465 ASP A 185 REMARK 465 ALA A 186 REMARK 465 GLY A 187 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 OD1 ASP A 8 OH TYR A 177 1.99 REMARK 500 OE1 GLU A 46 O HOH A 301 2.05 REMARK 500 O HOH A 349 O HOH A 421 2.10 REMARK 500 O HOH A 430 O HOH A 437 2.11 REMARK 500 O HOH A 417 O HOH A 430 2.11 REMARK 500 O HOH A 390 O HOH A 408 2.12 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 ASN A 86 32.53 -97.07 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 = 6.67 ANGSTROMS DBREF 7O1D A 1 242 PDB 7O1D 7O1D 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 ALA LYS VAL HIS LEU LYS ILE SEQRES 3 A 242 MET GLU GLU VAL LEU GLY ASP TYR PRO LEU ASN PRO LYS SEQRES 4 A 242 THR LEU LEU ASP GLU TYR GLU LYS LEU ALA ARG GLU ALA SEQRES 5 A 242 PHE SER ASN TYR ALA GLY LYS PRO TYR ARG PRO LEU ARG SEQRES 6 A 242 ASP ILE LEU GLU GLU VAL MET ARG LYS LEU ALA GLU LYS SEQRES 7 A 242 TYR GLY PHE LYS TYR PRO GLU ASN LEU TRP GLU ILE SER SEQRES 8 A 242 LEU ARG MET ALA GLN ARG TYR GLY GLU 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 ARG ASP THR GLU PRO 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 PHE LYS PRO SEQRES 13 A 242 HIS PRO ARG ILE PHE 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 ILE 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 FORMUL 2 HOH *148(H2 O) HELIX 1 AA1 SER A 9 LEU A 13 5 5 HELIX 2 AA2 SER A 15 GLY A 32 1 18 HELIX 3 AA3 ASN A 37 ALA A 57 1 21 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 LYS A 113 1 10 HELIX 7 AA7 ASP A 125 LEU A 136 1 12 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 PRO A 158 GLY A 169 1 12 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 LEU A 219 GLN A 232 1 14 SHEET 1 AA1 6 SER A 144 THR A 147 0 SHEET 2 AA1 6 HIS A 117 LEU A 122 1 N LEU A 122 O THR A 146 SHEET 3 AA1 6 ALA A 4 PHE A 7 1 N PHE A 7 O ILE A 121 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 THR A 195 N TYR A 177 SHEET 6 AA1 6 PHE A 214 VAL A 216 1 O PHE A 214 N LEU A 198 CISPEP 1 LYS A 155 PRO A 156 0 5.27 CRYST1 36.560 69.630 45.720 90.00 99.29 90.00 P 1 21 1 2 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 0.027352 0.000000 0.004474 0.00000 SCALE2 0.000000 0.014362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022163 0.00000