HEADER SIGNALING PROTEIN 20-MAR-24 8YR7 TITLE CRYSTAL STRUCTURE OF HUMAN DISHEVELLED 2 (DVL2) PDZ DOMAIN FUSED WITH TITLE 2 WGEF INTERNAL PEPTIDE MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2,RHO COMPND 3 GUANINE NUCLEOTIDE EXCHANGE FACTOR 19; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: DISHEVELLED-2,DSH HOMOLOG 2,EPHEXIN-2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 32630, 9606; SOURCE 5 GENE: DVL2, ARHGEF19; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS WNT SIGNALING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.OMBLE,S.MAHAJAN,K.A.KULKARNI REVDAT 1 29-MAY-24 8YR7 0 JRNL AUTH A.OMBLE,S.MAHAJAN,A.BHOITE,K.KULKARNI JRNL TITL DISHEVELLED2 ACTIVATES WGEF VIA ITS INTERACTION WITH A JRNL TITL 2 UNIQUE INTERNAL PEPTIDE MOTIF OF THE GEF. JRNL REF COMMUN BIOL V. 7 543 2024 JRNL REFN ESSN 2399-3642 JRNL PMID 38714795 JRNL DOI 10.1038/S42003-024-06194-6 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 2067 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.301 REMARK 3 R VALUE (WORKING SET) : 0.300 REMARK 3 FREE R VALUE : 0.335 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.610 REMARK 3 FREE R VALUE TEST SET COUNT : 116 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 29.7500 - 6.0000 1.00 265 3 0.2754 0.3682 REMARK 3 2 5.9900 - 4.7800 1.00 237 26 0.3288 0.2801 REMARK 3 3 4.7600 - 4.1600 1.00 238 18 0.2691 0.2585 REMARK 3 4 4.1600 - 3.7800 1.00 249 7 0.3226 0.6701 REMARK 3 5 3.7800 - 3.5200 1.00 249 5 0.3231 0.3860 REMARK 3 6 3.5100 - 3.3100 1.00 230 28 0.3126 0.5196 REMARK 3 7 3.3100 - 3.1400 1.00 244 14 0.3601 0.3114 REMARK 3 8 3.1400 - 3.0000 1.00 239 15 0.3633 0.3315 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.566 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.3 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 : 0.009 512 REMARK 3 ANGLE : 1.361 697 REMARK 3 CHIRALITY : 0.090 96 REMARK 3 PLANARITY : 0.004 88 REMARK 3 DIHEDRAL : 10.710 161 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 17.2095 -1.2602 2.0149 REMARK 3 T TENSOR REMARK 3 T11: 0.6839 T22: 1.1836 REMARK 3 T33: 0.7828 T12: 0.0251 REMARK 3 T13: 0.2796 T23: 0.0511 REMARK 3 L TENSOR REMARK 3 L11: 12.7200 L22: 9.5346 REMARK 3 L33: 13.2157 L12: 2.6339 REMARK 3 L13: 3.8814 L23: -0.9493 REMARK 3 S TENSOR REMARK 3 S11: 0.7991 S12: 1.7883 S13: 1.5462 REMARK 3 S21: 0.5646 S22: -0.9100 S23: 0.8022 REMARK 3 S31: 0.3050 S32: -0.2661 S33: 0.0215 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 8YR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2071 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.10 REMARK 200 R MERGE FOR SHELL (I) : 1.09100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE (PH 4.5), 3M REMARK 280 SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 29.74550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 29.74550 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.12500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.74550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.56250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.74550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.68750 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.74550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.74550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.12500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 29.74550 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 43.68750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 29.74550 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 14.56250 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 260 REMARK 465 MET A 261 REMARK 465 SER A 262 REMARK 465 LEU A 263 REMARK 465 TYR A 275 REMARK 465 ASN A 276 REMARK 465 SER A 286 REMARK 465 ASN A 287 REMARK 465 GLU A 288 REMARK 465 ARG A 289 REMARK 465 GLY A 290 REMARK 465 ASP A 291 REMARK 465 GLY A 292 REMARK 465 HIS A 342 REMARK 465 LYS A 343 REMARK 465 PRO A 344 REMARK 465 GLY A 355 REMARK 465 GLY A 356 REMARK 465 GLY A 357 REMARK 465 GLY A 358 REMARK 465 SER A 359 REMARK 465 THR A 360 REMARK 465 PHE A 361 REMARK 465 SER A 362 REMARK 465 LEU A 363 REMARK 465 TRP A 364 REMARK 465 GLN A 365 REMARK 465 ASP A 366 REMARK 465 ILE A 367 REMARK 465 PRO A 368 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 LEU A 270 CG CD1 CD2 REMARK 470 ASN A 271 CG OD1 ND2 REMARK 470 MET A 272 CG SD CE REMARK 470 GLU A 273 CG CD OE1 OE2 REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 PHE A 277 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 285 CD OE1 NE2 REMARK 470 MET A 300 CG SD CE REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 ARG A 310 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 312 CG CD OE1 OE2 REMARK 470 ASP A 322 CG OD1 OD2 REMARK 470 GLU A 326 CG CD OE1 OE2 REMARK 470 ASN A 327 CG OD1 ND2 REMARK 470 ASP A 331 CG OD1 OD2 REMARK 470 ARG A 335 CD NE CZ NH1 NH2 REMARK 470 ARG A 338 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 339 OD1 OD2 REMARK 470 VAL A 348 CG1 CG2 REMARK 470 LYS A 353 CG 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 ASN A 271 157.84 176.05 REMARK 500 GLU A 273 -113.45 51.10 REMARK 500 ASP A 322 5.29 58.27 REMARK 500 ASN A 327 -47.98 70.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YR7 A 261 353 UNP O14641 DVL2_HUMAN 261 353 DBREF 8YR7 A 358 368 UNP Q8IW93 ARHGJ_HUMAN 349 359 SEQADV 8YR7 SER A 260 UNP O14641 EXPRESSION TAG SEQADV 8YR7 SER A 354 UNP O14641 LINKER SEQADV 8YR7 GLY A 355 UNP O14641 LINKER SEQADV 8YR7 GLY A 356 UNP O14641 LINKER SEQADV 8YR7 GLY A 357 UNP O14641 LINKER SEQRES 1 A 109 SER MET SER LEU ASN ILE ILE THR VAL THR LEU ASN MET SEQRES 2 A 109 GLU LYS TYR ASN PHE LEU GLY ILE SER ILE VAL GLY GLN SEQRES 3 A 109 SER ASN GLU ARG GLY ASP GLY GLY ILE TYR ILE GLY SER SEQRES 4 A 109 ILE MET LYS GLY GLY ALA VAL ALA ALA ASP GLY ARG ILE SEQRES 5 A 109 GLU PRO GLY ASP MET LEU LEU GLN VAL ASN ASP MET ASN SEQRES 6 A 109 PHE GLU ASN MET SER ASN ASP ASP ALA VAL ARG VAL LEU SEQRES 7 A 109 ARG ASP ILE VAL HIS LYS PRO GLY PRO ILE VAL LEU THR SEQRES 8 A 109 VAL ALA LYS SER GLY GLY GLY GLY SER THR PHE SER LEU SEQRES 9 A 109 TRP GLN ASP ILE PRO HELIX 1 AA1 GLY A 303 GLY A 309 1 7 HELIX 2 AA2 SER A 329 VAL A 341 1 13 SHEET 1 AA1 4 ILE A 265 ILE A 266 0 SHEET 2 AA1 4 LEU A 349 ALA A 352 -1 O VAL A 351 N ILE A 266 SHEET 3 AA1 4 MET A 316 VAL A 320 -1 N GLN A 319 O THR A 350 SHEET 4 AA1 4 MET A 323 ASN A 324 -1 O MET A 323 N VAL A 320 SHEET 1 AA2 2 ILE A 280 VAL A 283 0 SHEET 2 AA2 2 TYR A 295 ILE A 299 -1 O TYR A 295 N VAL A 283 CRYST1 59.491 59.491 58.250 90.00 90.00 90.00 I 41 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 0.016809 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016809 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017167 0.00000