HEADER PLANT PROTEIN 14-JAN-24 8VO3 TITLE PATHOGENESIS RELATED 10-10 C59S MUTANT PAPAVERINE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PATHOGENESIS RELATED 10-10 C59S MUTANT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAPAVER SOMNIFERUM; SOURCE 3 ORGANISM_TAXID: 3469; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OPIUM POPPY, PAPAVER SOMNIFERUM, BENZYLISOQUINOLINE ALKALOID, BINDING KEYWDS 2 PROTEIN, LATEX, PATHOGENESIS RELATED PROTEIN, MAJOR LATEX PROTEIN, KEYWDS 3 PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.C.CARR,K.K.S.NG REVDAT 1 23-OCT-24 8VO3 0 JRNL AUTH S.C.CARR,P.J.FACCHINI,K.K.S.NG JRNL TITL STRUCTURAL ANALYSIS OF A LIGAND-TRIGGERED INTERMOLECULAR JRNL TITL 2 DISULFIDE SWITCH IN A MAJOR LATEX PROTEIN FROM OPIUM POPPY. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 80 675 2024 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 39207895 JRNL DOI 10.1107/S2059798324007733 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 25857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.730 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 36.9200 - 3.6100 0.99 1831 154 0.1864 0.2114 REMARK 3 2 3.6100 - 2.8600 1.00 1764 148 0.1958 0.2263 REMARK 3 3 2.8600 - 2.5000 1.00 1760 147 0.2173 0.2531 REMARK 3 4 2.5000 - 2.2700 1.00 1717 144 0.2152 0.2305 REMARK 3 5 2.2700 - 2.1100 1.00 1743 146 0.2090 0.2784 REMARK 3 6 2.1100 - 1.9900 1.00 1711 144 0.2152 0.2421 REMARK 3 7 1.9900 - 1.8900 1.00 1708 142 0.2456 0.2526 REMARK 3 8 1.8900 - 1.8000 1.00 1712 144 0.2324 0.2528 REMARK 3 9 1.8000 - 1.7400 0.99 1718 144 0.2356 0.2951 REMARK 3 10 1.7400 - 1.6800 1.00 1726 145 0.2522 0.3438 REMARK 3 11 1.6800 - 1.6200 1.00 1698 141 0.2514 0.3009 REMARK 3 12 1.6200 - 1.5800 0.99 1713 143 0.2647 0.2778 REMARK 3 13 1.5800 - 1.5400 0.95 1603 136 0.2715 0.2737 REMARK 3 14 1.5300 - 1.5000 0.84 1454 121 0.3009 0.3146 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) : 0.198 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.485 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.82 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 : 0.009 1219 REMARK 3 ANGLE : 1.131 1657 REMARK 3 CHIRALITY : 0.101 184 REMARK 3 PLANARITY : 0.006 209 REMARK 3 DIHEDRAL : 14.050 432 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 8VO3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1000278804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25890 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 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) : 1.05700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM PAPAVERINE, 10% METHANOL, 17% REMARK 280 (W/V) POLYETHYLENE GLYCOL 3350, AND 0.1M BIS-TRIS PH 5.1, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.13250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.13250 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 1.000000 0.000000 0.000000 24.38350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.74550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.38350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.74550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.13250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.38350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.74550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.13250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.38350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.74550 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 46.13250 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 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 GLY A 5 REMARK 465 VAL A 6 REMARK 465 SER A 7 REMARK 465 GLU A 34 REMARK 465 GLU A 35 REMARK 465 VAL A 36 REMARK 465 GLY A 115 REMARK 465 HIS A 116 REMARK 465 ALA A 158 DBREF 8VO3 A 1 158 PDB 8VO3 8VO3 1 158 SEQRES 1 A 158 MET ALA HIS HIS GLY VAL SER GLY LEU VAL GLY LYS LEU SEQRES 2 A 158 VAL THR GLN LEU GLU VAL ASN CYS ASP ALA ASP ILE PHE SEQRES 3 A 158 TYR LYS ILE VAL LYS HIS HIS GLU GLU VAL PRO ASN VAL SEQRES 4 A 158 ILE PRO HIS PHE PHE THR GLY VAL GLN VAL THR LYS GLY SEQRES 5 A 158 ASP GLY LEU VAL SER GLY SER ILE LYS GLU TRP ASN TYR SEQRES 6 A 158 VAL LEU GLU GLY LYS ALA MET THR ALA VAL GLU GLU THR SEQRES 7 A 158 THR HIS ALA ASP GLU THR ARG THR LEU THR HIS HIS ILE SEQRES 8 A 158 THR GLU GLY ASP ALA MET LYS ASP TYR LYS LYS PHE ASP SEQRES 9 A 158 VAL ILE VAL GLU THR ASN PRO LYS PRO ASN GLY HIS GLY SEQRES 10 A 158 SER VAL VAL THR TYR SER ILE VAL TYR GLU LYS ILE ASN SEQRES 11 A 158 GLU ASP SER PRO ALA PRO PHE ASP TYR LEU LYS PHE PHE SEQRES 12 A 158 HIS GLN ASN ILE VAL ASP MET SER ALA HIS ILE CYS SER SEQRES 13 A 158 SER ALA HET EV1 A 201 25 HETNAM EV1 1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE HETSYN EV1 PAPAVERINE FORMUL 2 EV1 C20 H21 N O4 FORMUL 3 HOH *115(H2 O) HELIX 1 AA1 ASP A 22 HIS A 32 1 11 HELIX 2 AA2 ASP A 82 THR A 84 5 3 HELIX 3 AA3 ALA A 96 LYS A 98 5 3 HELIX 4 AA4 PRO A 136 HIS A 153 1 18 SHEET 1 AA1 7 VAL A 10 VAL A 19 0 SHEET 2 AA1 7 SER A 118 LYS A 128 -1 O SER A 118 N VAL A 19 SHEET 3 AA1 7 TYR A 100 PRO A 111 -1 N ASN A 110 O VAL A 119 SHEET 4 AA1 7 THR A 86 GLY A 94 -1 N LEU A 87 O VAL A 107 SHEET 5 AA1 7 LYS A 70 ALA A 81 -1 N GLU A 77 O HIS A 90 SHEET 6 AA1 7 VAL A 56 LEU A 67 -1 N TYR A 65 O MET A 72 SHEET 7 AA1 7 HIS A 42 THR A 50 -1 N THR A 45 O GLU A 62 CRYST1 48.767 71.491 92.265 90.00 90.00 90.00 C 2 2 21 8 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 0.020506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010838 0.00000