HEADER SIGNALING PROTEIN 26-OCT-23 8WWR TITLE CRYSTAL STRUCTURE OF APO HUMAN DISHEVELLED 2 (DVL2) PDZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DISHEVELLED-2,DSH HOMOLOG 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DVL2; 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 8WWR 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8984 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.340 REMARK 3 FREE R VALUE TEST SET COUNT : 390 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 32.5100 - 3.7700 1.00 958 36 0.2166 0.2221 REMARK 3 2 3.7700 - 2.9900 1.00 882 46 0.2082 0.2423 REMARK 3 3 2.9900 - 2.6200 1.00 867 36 0.2360 0.2642 REMARK 3 4 2.6100 - 2.3800 1.00 864 36 0.2429 0.2714 REMARK 3 5 2.3700 - 2.2100 1.00 840 40 0.2415 0.2322 REMARK 3 6 2.2000 - 2.0800 1.00 844 40 0.2459 0.2921 REMARK 3 7 2.0700 - 1.9700 1.00 851 30 0.2406 0.2939 REMARK 3 8 1.9700 - 1.8900 1.00 838 44 0.2209 0.3074 REMARK 3 9 1.8900 - 1.8100 1.00 830 40 0.2488 0.3365 REMARK 3 10 1.8100 - 1.7500 1.00 820 42 0.2705 0.3322 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) : 0.195 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.082 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.78 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 : 0.007 624 REMARK 3 ANGLE : 1.089 841 REMARK 3 CHIRALITY : 0.065 106 REMARK 3 PLANARITY : 0.006 106 REMARK 3 DIHEDRAL : 6.627 89 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): 8.5030 -4.1046 -7.0590 REMARK 3 T TENSOR REMARK 3 T11: 0.1968 T22: 0.1507 REMARK 3 T33: 0.1899 T12: -0.0171 REMARK 3 T13: 0.0202 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 1.9911 L22: 3.3372 REMARK 3 L33: 3.3700 L12: -0.8827 REMARK 3 L13: -0.4723 L23: 2.2517 REMARK 3 S TENSOR REMARK 3 S11: -0.0489 S12: -0.1387 S13: -0.0192 REMARK 3 S21: 0.1575 S22: 0.0927 S23: 0.0706 REMARK 3 S31: 0.1213 S32: -0.0569 S33: -0.0522 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 8WWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1300042158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-23 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87313 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9023 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 32.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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 (%): 39.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-SODIUM CITRATE, PH 5.6 20% REMARK 280 (V/V) ISOPROPANOL 20%(W/V) PEG4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.21100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.98900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.98900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.81650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.98900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.98900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.60550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.98900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.98900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.81650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.98900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.98900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.60550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.21100 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 286 REMARK 465 ASN A 287 REMARK 465 GLU A 288 REMARK 465 ARG A 289 REMARK 465 GLY A 290 REMARK 465 HIS A 342 REMARK 465 LYS A 343 REMARK 465 PRO A 344 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 GLU A 273 CG CD OE1 OE2 REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 GLN A 285 CD OE1 NE2 REMARK 470 ASP A 291 CG OD1 OD2 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 ASP A 339 OD1 OD2 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 ASP A 322 5.35 59.21 REMARK 500 SER A 329 173.64 -59.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 8WWR A 261 354 UNP O14641 DVL2_HUMAN 261 354 SEQADV 8WWR SER A 260 UNP O14641 EXPRESSION TAG SEQRES 1 A 95 SER MET SER LEU ASN ILE ILE THR VAL THR LEU ASN MET SEQRES 2 A 95 GLU LYS TYR ASN PHE LEU GLY ILE SER ILE VAL GLY GLN SEQRES 3 A 95 SER ASN GLU ARG GLY ASP GLY GLY ILE TYR ILE GLY SER SEQRES 4 A 95 ILE MET LYS GLY GLY ALA VAL ALA ALA ASP GLY ARG ILE SEQRES 5 A 95 GLU PRO GLY ASP MET LEU LEU GLN VAL ASN ASP MET ASN SEQRES 6 A 95 PHE GLU ASN MET SER ASN ASP ASP ALA VAL ARG VAL LEU SEQRES 7 A 95 ARG ASP ILE VAL HIS LYS PRO GLY PRO ILE VAL LEU THR SEQRES 8 A 95 VAL ALA LYS CYS FORMUL 2 HOH *20(H2 O) HELIX 1 AA1 ASN A 271 TYR A 275 5 5 HELIX 2 AA2 GLY A 303 GLY A 309 1 7 HELIX 3 AA3 SER A 329 VAL A 341 1 13 SHEET 1 AA1 4 ILE A 265 LEU A 270 0 SHEET 2 AA1 4 ILE A 347 ALA A 352 -1 O LEU A 349 N VAL A 268 SHEET 3 AA1 4 MET A 316 VAL A 320 -1 N LEU A 318 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 GLY A 284 0 SHEET 2 AA2 2 ILE A 294 ILE A 299 -1 O GLY A 297 N SER A 281 CRYST1 45.978 45.978 78.422 90.00 90.00 90.00 P 43 21 2 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 0.021750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012752 0.00000