HEADER SIGNALING PROTEIN 06-JAN-25 9LDN TITLE VERTICILLIUM EFFECTOR PEVD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EFFECTOR PROTEIN PEVD1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HYPERSENSITIVE RESPONSE-INDUCING PROTEIN PEVD1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VERTICILLIUM DAHLIAE; SOURCE 3 ORGANISM_COMMON: VERTICILLIUM WILT; SOURCE 4 ORGANISM_TAXID: 27337; SOURCE 5 GENE: PEVD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EFFECTOR PROTEIN HYPERSENSITIVE RESPONSE INDUCTION FLOWERING KEYWDS 2 PROMOTION C2 DOMAIN-LIKE STRUCTURE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.YANG,X.L.ZHANG,L.LIU,C.XU,F.BAI REVDAT 1 15-JUL-26 9LDN 0 JRNL AUTH X.YANG,X.L.ZHANG,F.BAI JRNL TITL RESEARCH ON THE MOLECULAR MECHANISM OF VERTICILLIUM WILT IN JRNL TITL 2 ARABIDOPSIS MEDIATED BY FUNGAL EFFECTOR PROTEIN PEVD1 AND JRNL TITL 3 DRUG MOLECULE DESIGN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: 000) 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 1492 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 35.8500 - 3.0000 1.00 2607 147 0.1980 0.2307 REMARK 3 2 3.0000 - 2.3800 1.00 2527 124 0.2337 0.2784 REMARK 3 3 2.3800 - 2.0800 1.00 2490 122 0.2266 0.2182 REMARK 3 4 2.0800 - 1.8900 1.00 2461 128 0.2015 0.1937 REMARK 3 5 1.8900 - 1.7600 1.00 2451 147 0.2229 0.2311 REMARK 3 6 1.7600 - 1.6500 1.00 2445 141 0.2416 0.2624 REMARK 3 7 1.6500 - 1.5700 1.00 2452 139 0.2341 0.2114 REMARK 3 8 1.5700 - 1.5000 1.00 2414 154 0.2237 0.2413 REMARK 3 9 1.5000 - 1.4400 1.00 2452 136 0.2214 0.2333 REMARK 3 10 1.4400 - 1.3900 1.00 2432 124 0.2587 0.2921 REMARK 3 11 1.3900 - 1.3500 1.00 2430 130 0.3303 0.4086 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 952 REMARK 3 ANGLE : 0.948 1290 REMARK 3 CHIRALITY : 0.081 138 REMARK 3 PLANARITY : 0.005 174 REMARK 3 DIHEDRAL : 6.262 130 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 9LDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 10-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPX BETA3 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 7.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32006 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX (1.19.2_4158: 000) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M SODIUM FORMATE, EVAPORATION, REMARK 280 TEMPERATURE 289K 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 27.64050 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 27.64050 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 29.20350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.79600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.20350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.79600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.64050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.20350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.79600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.64050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.20350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.79600 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: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 79.59200 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 MET A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 ALA A 19 REMARK 465 PRO A 20 REMARK 465 ALA A 21 REMARK 465 SER A 22 REMARK 465 PRO A 23 REMARK 465 GLY A 24 REMARK 465 SER A 25 REMARK 465 THR A 26 REMARK 465 GLY A 27 REMARK 465 ALA A 28 REMARK 465 PRO A 29 REMARK 465 PRO A 30 REMARK 465 ALA A 153 REMARK 465 GLU A 154 REMARK 465 ALA A 155 DBREF 9LDN A 19 155 UNP G0Y276 PEVD1_VERDA 19 155 SEQADV 9LDN MET A 12 UNP G0Y276 INITIATING METHIONINE SEQADV 9LDN HIS A 13 UNP G0Y276 EXPRESSION TAG SEQADV 9LDN HIS A 14 UNP G0Y276 EXPRESSION TAG SEQADV 9LDN HIS A 15 UNP G0Y276 EXPRESSION TAG SEQADV 9LDN HIS A 16 UNP G0Y276 EXPRESSION TAG SEQADV 9LDN HIS A 17 UNP G0Y276 EXPRESSION TAG SEQADV 9LDN HIS A 18 UNP G0Y276 EXPRESSION TAG SEQRES 1 A 144 MET HIS HIS HIS HIS HIS HIS ALA PRO ALA SER PRO GLY SEQRES 2 A 144 SER THR GLY ALA PRO PRO ASP PRO ASN MET TYR GLU ASN SEQRES 3 A 144 ILE ASP ILE ALA ASP PHE ASN VAL ARG LYS GLY GLU ASP SEQRES 4 A 144 GLY THR ILE LYS TYR VAL ASN PHE LYS LEU SER GLY ASP SEQRES 5 A 144 ASP ALA ASP GLY LEU LEU CYS GLU ALA GLN ASN PRO GLY SEQRES 6 A 144 LEU PRO SER ASN VAL ILE THR CYS GLY GLU SER LYS TYR SEQRES 7 A 144 ARG PHE ALA LEU SER SER GLY LYS GLN TYR GLU PHE ALA SEQRES 8 A 144 LEU SER LEU TYR HIS GLU LEU GLY LEU ALA VAL GLY PHE SEQRES 9 A 144 TYR GLY THR GLY GLU ILE PHE THR HIS CYS ARG ALA GLY SEQRES 10 A 144 GLY LEU GLY ASP PHE ILE CYS GLN GLN GLN ASN PRO THR SEQRES 11 A 144 THR ILE VAL ILE ASP SER LEU PRO ASP ALA PRO ALA GLU SEQRES 12 A 144 ALA FORMUL 2 HOH *61(H2 O) SHEET 1 AA1 5 ALA A 65 GLN A 73 0 SHEET 2 AA1 5 ILE A 53 GLY A 62 -1 N LEU A 60 O LEU A 68 SHEET 3 AA1 5 TYR A 35 LYS A 47 -1 N ALA A 41 O LYS A 59 SHEET 4 AA1 5 ASP A 132 GLN A 137 -1 O CYS A 135 N VAL A 45 SHEET 5 AA1 5 THR A 123 GLY A 129 -1 N ARG A 126 O ILE A 134 SHEET 1 AA2 4 ALA A 65 GLN A 73 0 SHEET 2 AA2 4 ILE A 53 GLY A 62 -1 N LEU A 60 O LEU A 68 SHEET 3 AA2 4 TYR A 35 LYS A 47 -1 N ALA A 41 O LYS A 59 SHEET 4 AA2 4 THR A 141 ASP A 146 -1 O ILE A 143 N ILE A 38 SHEET 1 AA3 4 ILE A 82 THR A 83 0 SHEET 2 AA3 4 TYR A 89 SER A 95 -1 O PHE A 91 N ILE A 82 SHEET 3 AA3 4 PHE A 101 HIS A 107 -1 O ALA A 102 N SER A 94 SHEET 4 AA3 4 PHE A 115 ILE A 121 -1 O GLY A 119 N LEU A 103 SSBOND 1 CYS A 70 CYS A 84 1555 1555 2.04 SSBOND 2 CYS A 125 CYS A 135 1555 1555 2.06 CISPEP 1 LEU A 77 PRO A 78 0 0.80 CRYST1 58.407 79.592 55.281 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 0.017121 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018089 0.00000 CONECT 312 411 CONECT 411 312 CONECT 735 804 CONECT 804 735 MASTER 250 0 0 0 13 0 0 6 993 1 4 12 END