HEADER DE NOVO PROTEIN 09-JUN-21 7F1H TITLE DESIGNED ENZYME RA61 M48K/I72D MUTANT: FORM I COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENGINEERED RETROALDOLASE; 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; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALDOL REACTION, RETRO-ALDOL REACTION, MUTATION, REACTION DIRECTION, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.FUJIOKA,M.OKA,N.NUMOTO,N.ITO,M.ODA,F.TANAKA REVDAT 4 29-NOV-23 7F1H 1 REMARK REVDAT 3 16-MAR-22 7F1H 1 JRNL REVDAT 2 16-FEB-22 7F1H 1 JRNL REVDAT 1 24-NOV-21 7F1H 0 JRNL AUTH T.FUJIOKA,N.NUMOTO,H.AKAMA,K.SHILPA,M.OKA,P.K.ROY,Y.KRISHNA, JRNL AUTH 2 N.ITO,D.BAKER,M.ODA,F.TANAKA JRNL TITL VARYING THE DIRECTIONALITY OF PROTEIN CATALYSTS FOR ALDOL JRNL TITL 2 AND RETRO-ALDOL REACTIONS. JRNL REF CHEMBIOCHEM V. 23 00435 2022 JRNL REFN ESSN 1439-7633 JRNL PMID 34698422 JRNL DOI 10.1002/CBIC.202100435 REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 60103 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3013 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 39.8300 - 3.1800 0.99 2895 159 0.1346 0.1385 REMARK 3 2 3.1800 - 2.5200 0.99 2860 140 0.1440 0.1762 REMARK 3 3 2.5200 - 2.2100 1.00 2875 154 0.1323 0.1381 REMARK 3 4 2.2100 - 2.0000 1.00 2855 153 0.1144 0.1474 REMARK 3 5 2.0000 - 1.8600 0.99 2820 144 0.1129 0.1259 REMARK 3 6 1.8600 - 1.7500 1.00 2854 159 0.1178 0.1316 REMARK 3 7 1.7500 - 1.6600 1.00 2853 140 0.1108 0.1459 REMARK 3 8 1.6600 - 1.5900 1.00 2853 162 0.1051 0.1360 REMARK 3 9 1.5900 - 1.5300 1.00 2827 137 0.1041 0.1253 REMARK 3 10 1.5300 - 1.4800 1.00 2844 167 0.1059 0.1398 REMARK 3 11 1.4800 - 1.4300 1.00 2827 151 0.1092 0.1523 REMARK 3 12 1.4300 - 1.3900 1.00 2876 152 0.1098 0.1353 REMARK 3 13 1.3900 - 1.3500 1.00 2830 134 0.1127 0.1301 REMARK 3 14 1.3500 - 1.3200 1.00 2836 163 0.1171 0.1497 REMARK 3 15 1.3200 - 1.2900 1.00 2840 143 0.1136 0.1717 REMARK 3 16 1.2900 - 1.2600 1.00 2841 154 0.1240 0.1531 REMARK 3 17 1.2600 - 1.2400 0.99 2835 146 0.1310 0.1648 REMARK 3 18 1.2400 - 1.2100 0.92 2621 143 0.1398 0.1706 REMARK 3 19 1.2100 - 1.1900 0.74 2119 109 0.1377 0.2156 REMARK 3 20 1.1900 - 1.1700 0.63 1786 89 0.1439 0.1643 REMARK 3 21 1.1700 - 1.1500 0.51 1430 84 0.1639 0.1767 REMARK 3 22 1.1500 - 1.1400 0.25 713 30 0.1790 0.2551 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) : 0.076 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.997 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.11 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 : 0.005 1573 REMARK 3 ANGLE : 0.940 2141 REMARK 3 CHIRALITY : 0.084 220 REMARK 3 PLANARITY : 0.006 269 REMARK 3 DIHEDRAL : 13.425 530 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 7F1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022666. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 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 : 3.300 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: 3B5L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 2.0 M AMMONIUM REMARK 280 FORMATE, 8.6 MM ETHYL 6,6,6-TRIFLUORO-5-HYDROXY-3-OXO-5-PHENYL- REMARK 280 HEXANOATE, VAPOR DIFFUSION, TEMPERATURE 293K 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 32.11800 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: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLU A 190 REMARK 465 GLY A 191 REMARK 465 GLY A 192 REMARK 465 ASN A 193 REMARK 465 PRO A 194 REMARK 465 GLY A 195 REMARK 465 ASN A 196 REMARK 465 PRO A 197 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 33 126.38 -31.47 REMARK 500 ASP A 169 -148.98 -104.48 REMARK 500 GLN A 179 -177.68 69.66 REMARK 500 SER A 180 -157.02 58.63 REMARK 500 SER A 180 -156.45 57.65 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 593 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 594 DISTANCE = 6.26 ANGSTROMS DBREF 7F1H A -3 197 PDB 7F1H 7F1H -3 197 SEQRES 1 A 201 GLY SER HIS MET ASP THR THR ILE THR GLN ASN GLN THR SEQRES 2 A 201 GLY TYR ASP ASN GLY TYR PHE TYR SER PHE TRP THR ASP SEQRES 3 A 201 ALA PRO GLY THR VAL SER MET THR LEU HIS SER GLY GLY SEQRES 4 A 201 SER TYR SER THR SER TRP ARG ASN THR GLY HIS PHE LYS SEQRES 5 A 201 ALA GLY LYS GLY TRP SER THR GLY GLY ARG ARG THR VAL SEQRES 6 A 201 THR TYR ASN ALA SER PHE ASN PRO SER GLY ASP ALA TYR SEQRES 7 A 201 LEU THR LEU TYR GLY TRP THR ARG ASN PRO LEU VAL SER SEQRES 8 A 201 TYR LEU ILE VAL GLU SER TRP GLY THR TYR ARG PRO THR SEQRES 9 A 201 GLY THR TYR LYS GLY THR VAL THR THR ASP GLY GLY THR SEQRES 10 A 201 TYR ASP ILE TYR GLU THR TRP ARG TYR ASN ALA PRO SER SEQRES 11 A 201 ILE GLU GLY THR ARG THR PHE GLN ILE PHE TRP SER VAL SEQRES 12 A 201 ARG GLN GLN LYS ARG THR SER GLY THR ILE THR ILE GLY SEQRES 13 A 201 ASN HIS PHE ASP ALA TRP ALA ARG ALA GLY MET ASN LEU SEQRES 14 A 201 GLY SER HIS ASP TYR GLN ILE MET ALA THR LYS GLY TRP SEQRES 15 A 201 GLN SER SER GLY SER SER THR VAL SER ILE SER GLU GLY SEQRES 16 A 201 GLY ASN PRO GLY ASN PRO HET FMT A 201 3 HET FMT A 202 3 HET FMT A 203 3 HET FMT A 204 3 HET FMT A 205 3 HET GOL A 206 6 HETNAM FMT FORMIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FMT 5(C H2 O2) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *294(H2 O) HELIX 1 AA1 ILE A 151 ALA A 161 1 11 SHEET 1 AA1 6 THR A 2 ILE A 4 0 SHEET 2 AA1 6 VAL A 27 LEU A 31 -1 O MET A 29 N ILE A 4 SHEET 3 AA1 6 SER A 36 TRP A 41 -1 O SER A 40 N SER A 28 SHEET 4 AA1 6 GLY A 182 SER A 189 -1 O VAL A 186 N TYR A 37 SHEET 5 AA1 6 THR A 60 PRO A 69 -1 N THR A 62 O SER A 189 SHEET 6 AA1 6 SER A 146 THR A 150 -1 O ILE A 149 N VAL A 61 SHEET 1 AA2 9 GLN A 8 ASP A 12 0 SHEET 2 AA2 9 TYR A 15 THR A 21 -1 O TYR A 15 N ASP A 12 SHEET 3 AA2 9 HIS A 46 TRP A 53 -1 O GLY A 52 N PHE A 16 SHEET 4 AA2 9 SER A 167 TRP A 178 -1 O MET A 173 N LYS A 51 SHEET 5 AA2 9 ASP A 72 ARG A 82 -1 N THR A 76 O ALA A 174 SHEET 6 AA2 9 VAL A 86 TRP A 94 -1 O ILE A 90 N LEU A 77 SHEET 7 AA2 9 ARG A 131 ARG A 140 1 O SER A 138 N VAL A 91 SHEET 8 AA2 9 GLY A 112 ALA A 124 -1 N ALA A 124 O ARG A 131 SHEET 9 AA2 9 THR A 102 THR A 109 -1 N VAL A 107 O TYR A 114 CISPEP 1 ASN A 83 PRO A 84 0 7.19 CRYST1 35.644 64.236 42.682 90.00 111.07 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 0.028055 0.000000 0.010811 0.00000 SCALE2 0.000000 0.015568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025108 0.00000