HEADER PLANT PROTEIN 23-APR-19 6OOD TITLE STRUCTURE OF THE PTEROCARPAN SYNTHASE DIRIGENT PROTEIN PSPTS1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PTEROCARPAN SYNTHASE DIRIGENT PROTEIN PSPTS1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 3 ORGANISM_TAXID: 3888; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIRIGENT PROTEIN, APO-FORM, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH REVDAT 3 13-MAR-24 6OOD 1 REMARK REVDAT 2 11-NOV-20 6OOD 1 JRNL REVDAT 1 29-APR-20 6OOD 0 JRNL AUTH Q.MENG,S.G.A.MOINUDDIN,S.J.KIM,D.L.BEDGAR,M.A.COSTA, JRNL AUTH 2 D.G.THOMAS,R.P.YOUNG,C.A.SMITH,J.R.CORT,L.B.DAVIN,N.G.LEWIS JRNL TITL PTEROCARPAN SYNTHASE (PTS) STRUCTURES SUGGEST A COMMON JRNL TITL 2 QUINONE METHIDE-STABILIZING FUNCTION IN DIRIGENT PROTEINS JRNL TITL 3 AND PROTEINS WITH DIRIGENT-LIKE DOMAINS. JRNL REF J.BIOL.CHEM. V. 295 11584 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32565424 JRNL DOI 10.1074/JBC.RA120.012444 REMARK 2 REMARK 2 RESOLUTION. 1.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 26219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1315 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 35.2918 - 3.1196 1.00 2921 146 0.1435 0.1369 REMARK 3 2 3.1196 - 2.4763 1.00 2816 153 0.1630 0.2000 REMARK 3 3 2.4763 - 2.1634 0.97 2729 143 0.1981 0.2407 REMARK 3 4 2.1634 - 1.9656 1.00 2790 130 0.1474 0.2052 REMARK 3 5 1.9656 - 1.8247 0.94 2615 136 0.2307 0.2617 REMARK 3 6 1.8247 - 1.7171 1.00 2752 151 0.1369 0.1923 REMARK 3 7 1.7171 - 1.6311 1.00 2774 145 0.1446 0.2236 REMARK 3 8 1.6311 - 1.5601 1.00 2752 146 0.1584 0.2097 REMARK 3 9 1.5601 - 1.5001 1.00 2755 165 0.1665 0.2090 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.30 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 6OOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000241047. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27529 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 35.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M SODIUM ACETATE TRIHYDRATE, PH REMARK 280 4.9, 10 % (W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 39.44650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.44650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.44650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.44650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.44650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.44650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 39.44650 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 39.44650 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 39.44650 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 39.44650 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 39.44650 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 39.44650 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 39.44650 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 39.44650 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 39.44650 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 39.44650 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 39.44650 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 39.44650 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 370 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 484 LIES ON A SPECIAL POSITION. 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 MET A 22 REMARK 465 THR A 23 REMARK 465 LYS A 24 REMARK 465 TYR A 25 REMARK 465 TYR A 26 REMARK 465 GLN A 27 REMARK 465 SER A 28 REMARK 465 LEU A 29 REMARK 465 SER A 30 REMARK 465 PRO A 31 REMARK 465 THR A 32 REMARK 465 MET A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 GLU A 191 REMARK 465 LEU A 192 REMARK 465 ASN A 193 REMARK 465 SER A 194 REMARK 465 LYS A 195 REMARK 465 LEU A 196 REMARK 465 GLU A 197 REMARK 465 GLY A 198 REMARK 465 LYS A 199 REMARK 465 PRO A 200 REMARK 465 ILE A 201 REMARK 465 PRO A 202 REMARK 465 ASN A 203 REMARK 465 PRO A 204 REMARK 465 LEU A 205 REMARK 465 LEU A 206 REMARK 465 GLY A 207 REMARK 465 LEU A 208 REMARK 465 ASP A 209 REMARK 465 SER A 210 REMARK 465 THR A 211 REMARK 465 ARG A 212 REMARK 465 THR A 213 REMARK 465 GLY A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 HIS A 217 REMARK 465 HIS A 218 REMARK 465 HIS A 219 REMARK 465 HIS A 220 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 PHE A 126 49.32 -143.27 REMARK 500 PHE A 126 51.19 -144.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 6OOD A 22 220 PDB 6OOD 6OOD 22 220 SEQRES 1 A 199 MET THR LYS TYR TYR GLN SER LEU SER PRO THR MET LEU SEQRES 2 A 199 GLY PHE GLN GLU GLU LYS PHE THR HIS LEU HIS PHE TYR SEQRES 3 A 199 PHE HIS ASP ILE VAL THR GLY PRO LYS PRO SER MET VAL SEQRES 4 A 199 PHE VAL ALA GLU PRO ASN GLY LYS VAL GLU ASN ALA LEU SEQRES 5 A 199 PRO PHE GLY THR VAL VAL ALA MET ASP ASP PRO LEU THR SEQRES 6 A 199 ALA GLY PRO GLU ARG ASP SER LYS LEU VAL GLY LYS ALA SEQRES 7 A 199 GLN GLY ILE TYR THR SER ILE SER GLN GLU GLU MET GLY SEQRES 8 A 199 LEU MET MET VAL MET THR MET ALA PHE SER ASP GLY GLU SEQRES 9 A 199 PHE ASN GLY SER THR LEU SER ILE LEU GLY ARG ASN MET SEQRES 10 A 199 ILE MET SER GLU THR ILE ARG GLU MET ALA ILE VAL GLY SEQRES 11 A 199 GLY THR GLY ALA PHE ARG PHE VAL ARG GLY TYR ALA GLN SEQRES 12 A 199 ALA LYS PHE PHE SER VAL ASP PHE THR THR GLY ASP ALA SEQRES 13 A 199 THR VAL GLU TYR ASP ILE PHE VAL PHE HIS TYR LYS GLY SEQRES 14 A 199 GLU LEU ASN SER LYS LEU GLU GLY LYS PRO ILE PRO ASN SEQRES 15 A 199 PRO LEU LEU GLY LEU ASP SER THR ARG THR GLY HIS HIS SEQRES 16 A 199 HIS HIS HIS HIS FORMUL 2 HOH *184(H2 O) HELIX 1 AA1 GLY A 154 ARG A 157 5 4 SHEET 1 AA110 MET A 59 ALA A 63 0 SHEET 2 AA110 VAL A 78 THR A 86 -1 O VAL A 78 N VAL A 62 SHEET 3 AA110 LEU A 95 SER A 105 -1 O VAL A 96 N LEU A 85 SHEET 4 AA110 LEU A 113 PHE A 121 -1 O THR A 118 N GLN A 100 SHEET 5 AA110 THR A 130 ASN A 137 -1 O GLY A 135 N MET A 115 SHEET 6 AA110 ARG A 145 THR A 153 -1 O GLY A 151 N SER A 132 SHEET 7 AA110 ARG A 160 VAL A 170 -1 O ALA A 163 N MET A 147 SHEET 8 AA110 ALA A 177 HIS A 187 -1 O PHE A 186 N ARG A 160 SHEET 9 AA110 LYS A 40 ASP A 50 -1 N LEU A 44 O ILE A 183 SHEET 10 AA110 VAL A 78 THR A 86 -1 O THR A 86 N TYR A 47 CRYST1 78.893 78.893 78.893 90.00 90.00 90.00 P 21 3 12 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 0.012675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012675 0.00000