HEADER DE NOVO PROTEIN 09-JUN-21 7F1K TITLE DESIGNED ENZYME RA61 M48K/I72D MUTANT: FORM IV 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 7F1K 1 REMARK REVDAT 3 16-MAR-22 7F1K 1 JRNL REVDAT 2 16-FEB-22 7F1K 1 JRNL REVDAT 1 24-NOV-21 7F1K 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. 1.05 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 63890 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3198 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 17.5800 - 2.9800 0.97 2824 135 0.1295 0.1276 REMARK 3 2 2.9800 - 2.3700 0.98 2792 163 0.1490 0.1431 REMARK 3 3 2.3700 - 2.0700 0.96 2782 148 0.1404 0.1916 REMARK 3 4 2.0700 - 1.8800 0.95 2781 121 0.1295 0.1475 REMARK 3 5 1.8800 - 1.7500 0.95 2707 146 0.1411 0.1733 REMARK 3 6 1.7500 - 1.6400 0.94 2740 170 0.1446 0.1732 REMARK 3 7 1.6400 - 1.5600 0.95 2695 147 0.1340 0.1625 REMARK 3 8 1.5600 - 1.4900 0.94 2721 132 0.1327 0.1490 REMARK 3 9 1.4900 - 1.4400 0.94 2714 126 0.1421 0.2003 REMARK 3 10 1.4400 - 1.3900 0.93 2681 141 0.1459 0.2088 REMARK 3 11 1.3900 - 1.3400 0.93 2665 150 0.1573 0.1868 REMARK 3 12 1.3400 - 1.3000 0.92 2668 152 0.1641 0.2153 REMARK 3 13 1.3000 - 1.2700 0.92 2624 136 0.1777 0.2322 REMARK 3 14 1.2700 - 1.2400 0.91 2646 146 0.1820 0.2615 REMARK 3 15 1.2400 - 1.2100 0.90 2599 133 0.1866 0.2199 REMARK 3 16 1.2100 - 1.1900 0.90 2604 123 0.1981 0.2367 REMARK 3 17 1.1900 - 1.1600 0.90 2624 143 0.2089 0.2151 REMARK 3 18 1.1600 - 1.1400 0.89 2581 118 0.2135 0.2645 REMARK 3 19 1.1400 - 1.1200 0.87 2521 151 0.2326 0.2435 REMARK 3 20 1.1200 - 1.1000 0.87 2473 136 0.2487 0.2743 REMARK 3 21 1.1000 - 1.0800 0.86 2514 131 0.2742 0.3022 REMARK 3 22 1.0800 - 1.0700 0.86 2471 137 0.3096 0.3375 REMARK 3 23 1.0700 - 1.0500 0.79 2265 113 0.3655 0.3729 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) : 0.118 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.44 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 1682 REMARK 3 ANGLE : 0.964 2311 REMARK 3 CHIRALITY : 0.080 239 REMARK 3 PLANARITY : 0.005 296 REMARK 3 DIHEDRAL : 13.510 590 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 7F1K 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_1300022675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-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 : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64002 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 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 : 1.300 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 (%): 29.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRISODIUM CITRATE DIHYDRATE, PH REMARK 280 5.6, 20% (V/V) 2-PROPANOL, 20% (W/V) PEG4000, 1.7 MM ETHYL 6,6,6- REMARK 280 TRIFLUORO-5-HYDROXY-3-OXO-5-PHENYL-HEXANOATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 -3 REMARK 465 SER A -2 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 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 ARG A 42 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 176 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 ARG A 58 44.22 -85.28 REMARK 500 SER A 70 56.01 -107.23 REMARK 500 ARG A 131 -175.80 -171.21 REMARK 500 ASP A 169 -140.14 -106.31 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 414 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A 415 DISTANCE = 7.04 ANGSTROMS DBREF 7F1K A -3 197 PDB 7F1K 7F1K -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 FORMUL 2 HOH *215(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 38 N THR A 30 SHEET 4 AA1 6 GLY A 182 GLY A 191 -1 O VAL A 186 N TYR A 37 SHEET 5 AA1 6 THR A 60 PRO A 69 -1 N SER A 66 O THR A 185 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 GLN A 171 N TRP A 53 SHEET 5 AA2 9 ASP A 72 ARG A 82 -1 N TYR A 78 O ILE A 172 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 GLY A 105 O ILE A 116 CISPEP 1 ASN A 83 PRO A 84 0 4.79 CRYST1 33.226 36.805 37.544 111.99 96.51 109.19 P 1 1 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 0.030097 0.010476 0.008934 0.00000 SCALE2 0.000000 0.028769 0.014044 0.00000 SCALE3 0.000000 0.000000 0.029832 0.00000