HEADER PLANT PROTEIN 03-MAY-21 7EQL TITLE CRYSTAL STRUCTURE OF (+)-PULEGONE REDUCTASE FROM MENTHA PIPERITA COMPND MOL_ID: 1; COMPND 2 MOLECULE: (+)-PULEGONE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.3.1.81; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MENTHA PIPERITA; SOURCE 3 ORGANISM_COMMON: PEPPERMINT, MENTHA AQUATICA X MENTHA SPICATA; SOURCE 4 ORGANISM_TAXID: 34256; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DOUBLE BOND REDUCTASE, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.LIN REVDAT 4 29-NOV-23 7EQL 1 REMARK REVDAT 3 13-APR-22 7EQL 1 JRNL REVDAT 2 13-OCT-21 7EQL 1 JRNL REVDAT 1 29-SEP-21 7EQL 0 JRNL AUTH C.LIU,Q.GAO,Z.SHANG,J.LIU,S.ZHOU,J.DANG,L.LIU,I.LANGE, JRNL AUTH 2 N.SRIVIDYA,B.M.LANGE,Q.WU,W.LIN JRNL TITL FUNCTIONAL CHARACTERIZATION AND STRUCTURAL INSIGHTS INTO JRNL TITL 2 STEREOSELECTIVITY OF PULEGONE REDUCTASE IN MENTHOL JRNL TITL 3 BIOSYNTHESIS. JRNL REF FRONT PLANT SCI V. 12 80970 2021 JRNL REFN ESSN 1664-462X JRNL PMID 34917113 JRNL DOI 10.3389/FPLS.2021.780970 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 104.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 12422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.275 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.590 REMARK 3 FREE R VALUE TEST SET COUNT : 695 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 50.0000 - 4.6505 0.95 2388 135 0.2336 0.2693 REMARK 3 2 4.6505 - 3.6911 0.95 2330 115 0.2604 0.2604 REMARK 3 3 3.6911 - 3.2245 0.92 2238 145 0.3558 0.4328 REMARK 3 4 3.2245 - 2.9297 0.99 2359 161 0.3824 0.4188 REMARK 3 5 2.9297 - 2.7200 0.99 2412 139 0.3957 0.4029 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 112.2 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7EQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300021380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12444 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 104.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4HFJ REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M AMMONIUM SULFATE , 0.1 M BIS-TRIS REMARK 280 (PH 5.5), 1% W/V PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 38.41733 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 19.20867 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 0.00000 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 38.41733 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 19.20867 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 60.05550 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 104.01918 REMARK 350 BIOMT3 2 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 ILE A 63 REMARK 465 ILE A 69 REMARK 465 LEU A 70 REMARK 465 GLU A 342 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 PHE A 199 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 316 CG CD1 CD2 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 16 74.42 53.58 REMARK 500 CYS A 37 70.24 -154.03 REMARK 500 LEU A 46 -67.99 -135.60 REMARK 500 LYS A 60 22.06 80.30 REMARK 500 GLN A 65 -2.80 55.75 REMARK 500 ASP A 67 -70.07 -76.80 REMARK 500 SER A 77 -159.89 -158.13 REMARK 500 ASN A 112 78.31 -151.59 REMARK 500 TYR A 114 -57.02 -128.78 REMARK 500 LYS A 122 -134.26 57.50 REMARK 500 PHE A 144 -62.06 -90.79 REMARK 500 SER A 186 145.52 -170.22 REMARK 500 GLN A 261 70.16 50.11 REMARK 500 ASN A 267 34.91 -89.69 REMARK 500 GLU A 310 -167.01 -125.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EQL A 1 342 UNP Q6WAU0 PULR_MENPI 1 342 SEQRES 1 A 342 MET VAL MET ASN LYS GLN ILE VAL LEU ASN ASN TYR ILE SEQRES 2 A 342 ASN GLY SER LEU LYS GLN SER ASP LEU ALA LEU ARG THR SEQRES 3 A 342 SER THR ILE CYS MET GLU ILE PRO ASP GLY CYS ASN GLY SEQRES 4 A 342 ALA ILE LEU VAL LYS ASN LEU TYR LEU SER VAL ASN PRO SEQRES 5 A 342 TYR LEU ILE LEU ARG MET GLY LYS LEU ASP ILE PRO GLN SEQRES 6 A 342 PHE ASP SER ILE LEU PRO GLY SER THR ILE VAL SER TYR SEQRES 7 A 342 GLY VAL SER LYS VAL LEU ASP SER THR HIS PRO SER TYR SEQRES 8 A 342 GLU LYS GLY GLU LEU ILE TRP GLY SER GLN ALA GLY TRP SEQRES 9 A 342 GLU GLU TYR THR LEU ILE GLN ASN PRO TYR ASN LEU PHE SEQRES 10 A 342 LYS ILE GLN ASP LYS ASP VAL PRO LEU SER TYR TYR VAL SEQRES 11 A 342 GLY ILE LEU GLY MET PRO GLY MET THR ALA TYR ALA GLY SEQRES 12 A 342 PHE PHE GLU ILE CYS SER PRO LYS LYS GLY GLU THR VAL SEQRES 13 A 342 PHE VAL THR ALA ALA ALA GLY SER VAL GLY GLN LEU VAL SEQRES 14 A 342 GLY GLN PHE ALA LYS MET PHE GLY CYS TYR VAL VAL GLY SEQRES 15 A 342 SER ALA GLY SER LYS GLU LYS VAL ASP LEU LEU LYS ASN SEQRES 16 A 342 LYS PHE GLY PHE ASP ASP ALA PHE ASN TYR LYS GLU GLU SEQRES 17 A 342 SER ASP TYR ASP THR ALA LEU LYS ARG HIS PHE PRO GLU SEQRES 18 A 342 GLY ILE ASP ILE TYR PHE ASP ASN VAL GLY GLY LYS MET SEQRES 19 A 342 LEU GLU ALA VAL ILE ASN ASN MET ARG VAL HIS GLY ARG SEQRES 20 A 342 ILE ALA VAL CYS GLY MET VAL SER GLN TYR SER LEU LYS SEQRES 21 A 342 GLN PRO GLU GLY VAL HIS ASN LEU LEU LYS LEU ILE PRO SEQRES 22 A 342 LYS GLN ILE ARG MET GLN GLY PHE VAL VAL VAL ASP TYR SEQRES 23 A 342 TYR HIS LEU TYR PRO LYS PHE LEU GLU MET VAL LEU PRO SEQRES 24 A 342 ARG ILE LYS GLU GLY LYS VAL THR TYR VAL GLU ASP ILE SEQRES 25 A 342 SER GLU GLY LEU GLU SER ALA PRO SER ALA LEU LEU GLY SEQRES 26 A 342 VAL TYR VAL GLY ARG ASN VAL GLY ASN GLN VAL VAL ALA SEQRES 27 A 342 VAL SER ARG GLU HELIX 1 AA1 LYS A 18 SER A 20 5 3 HELIX 2 AA2 PRO A 52 ARG A 57 1 6 HELIX 3 AA3 PRO A 125 VAL A 130 5 6 HELIX 4 AA4 GLY A 134 GLU A 146 1 13 HELIX 5 AA5 VAL A 165 GLY A 177 1 13 HELIX 6 AA6 SER A 186 GLY A 198 1 13 HELIX 7 AA7 ASP A 210 PHE A 219 1 10 HELIX 8 AA8 GLY A 231 ASN A 241 1 11 HELIX 9 AA9 MET A 253 TYR A 257 5 5 HELIX 10 AB1 HIS A 266 ILE A 272 5 7 HELIX 11 AB2 VAL A 282 HIS A 288 5 7 HELIX 12 AB3 LEU A 289 LEU A 298 1 10 HELIX 13 AB4 SER A 318 VAL A 328 1 11 SHEET 1 AA1 2 VAL A 2 LEU A 9 0 SHEET 2 AA1 2 LEU A 22 ILE A 29 -1 O SER A 27 N ASN A 4 SHEET 1 AA2 5 TYR A 107 ILE A 110 0 SHEET 2 AA2 5 ILE A 41 VAL A 50 -1 N VAL A 43 O THR A 108 SHEET 3 AA2 5 VAL A 76 SER A 86 -1 O LEU A 84 N LEU A 42 SHEET 4 AA2 5 LEU A 96 GLY A 103 -1 O ALA A 102 N SER A 77 SHEET 5 AA2 5 PHE A 117 LYS A 118 -1 O PHE A 117 N TRP A 98 SHEET 1 AA3 4 TYR A 107 ILE A 110 0 SHEET 2 AA3 4 ILE A 41 VAL A 50 -1 N VAL A 43 O THR A 108 SHEET 3 AA3 4 ASN A 334 ALA A 338 -1 O VAL A 337 N LEU A 48 SHEET 4 AA3 4 GLU A 310 GLU A 314 1 N SER A 313 O VAL A 336 SHEET 1 AA4 6 ASP A 201 ASN A 204 0 SHEET 2 AA4 6 TYR A 179 ALA A 184 1 N ALA A 184 O PHE A 203 SHEET 3 AA4 6 THR A 155 THR A 159 1 N VAL A 156 O TYR A 179 SHEET 4 AA4 6 ILE A 223 ASP A 228 1 O PHE A 227 N PHE A 157 SHEET 5 AA4 6 MET A 242 VAL A 250 1 O ARG A 243 N ILE A 223 SHEET 6 AA4 6 ARG A 277 GLY A 280 1 O ARG A 277 N ILE A 248 CRYST1 120.111 120.111 57.626 90.00 90.00 120.00 P 62 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 0.008326 0.004807 0.000000 0.00000 SCALE2 0.000000 0.009614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017353 0.00000