HEADER SIGNALING PROTEIN 24-MAR-20 7BQF TITLE DIMERIZATION OF SAV1 WW TANDEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SALVADOR HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 45 KDA WW DOMAIN PROTEIN,MWW45; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SAV1, WW45, WWP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIPPO PATHWAY, WW DOMAIN, SAV1, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.LIN,M.ZHANG REVDAT 2 29-NOV-23 7BQF 1 REMARK REVDAT 1 23-SEP-20 7BQF 0 JRNL AUTH Z.LIN,R.XIE,K.GUAN,M.ZHANG JRNL TITL A WW TANDEM-MEDIATED DIMERIZATION MODE OF SAV1 ESSENTIAL FOR JRNL TITL 2 HIPPO SIGNALING. JRNL REF CELL REP V. 32 08118 2020 JRNL REFN ESSN 2211-1247 JRNL PMID 32905778 JRNL DOI 10.1016/J.CELREP.2020.108118 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692+SVN 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11842 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.083 REMARK 3 FREE R VALUE TEST SET COUNT : 1194 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 27.7000 - 3.5347 1.00 1288 144 0.1691 0.1865 REMARK 3 2 3.5347 - 2.8065 1.00 1226 142 0.2095 0.2103 REMARK 3 3 2.8065 - 2.4520 1.00 1203 136 0.2151 0.2321 REMARK 3 4 2.4520 - 2.2279 0.99 1194 132 0.2089 0.2572 REMARK 3 5 2.2279 - 2.0683 0.99 1182 131 0.2024 0.2771 REMARK 3 6 2.0683 - 1.9464 0.98 1162 130 0.2095 0.2328 REMARK 3 7 1.9464 - 1.8489 0.97 1153 130 0.2167 0.2848 REMARK 3 8 1.8489 - 1.7684 0.96 1136 126 0.2215 0.2565 REMARK 3 9 1.7684 - 1.7004 0.94 1104 123 0.2392 0.2922 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) : 0.201 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.75 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 : 0.007 733 REMARK 3 ANGLE : 0.971 1007 REMARK 3 CHIRALITY : 0.043 96 REMARK 3 PLANARITY : 0.006 132 REMARK 3 DIHEDRAL : 12.713 266 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): -3.7667 -8.0505 22.7085 REMARK 3 T TENSOR REMARK 3 T11: 0.1948 T22: 0.1870 REMARK 3 T33: 0.1801 T12: -0.0105 REMARK 3 T13: 0.0130 T23: 0.0455 REMARK 3 L TENSOR REMARK 3 L11: 1.0490 L22: 4.6013 REMARK 3 L33: 2.2113 L12: 0.5100 REMARK 3 L13: 0.0680 L23: 1.0962 REMARK 3 S TENSOR REMARK 3 S11: 0.0389 S12: 0.0034 S13: -0.0567 REMARK 3 S21: 0.1441 S22: 0.1353 S23: -0.0196 REMARK 3 S31: 0.0865 S32: -0.2323 S33: -0.1081 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 7BQF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-17 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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11842 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 : 18.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2YSB, 2DWV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% V/V 1,4-DIOXANE, 20% W/V PEG 3350 REMARK 280 AND 100 MM TRIS-HCL (PH 8.0), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.71700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.43400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.43400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.71700 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: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 55.43400 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 GLY A 194 REMARK 465 PRO A 195 REMARK 465 GLY A 196 REMARK 465 SER A 197 REMARK 465 GLU A 198 REMARK 465 GLN A 283 REMARK 465 PRO A 284 REMARK 465 GLN A 285 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 ASP A 199 CG OD1 OD2 REMARK 470 MET A 212 CG SD CE REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DIO A 301 DBREF 7BQF A 196 285 UNP Q8VEB2 SAV1_MOUSE 196 285 SEQADV 7BQF GLY A 194 UNP Q8VEB2 EXPRESSION TAG SEQADV 7BQF PRO A 195 UNP Q8VEB2 EXPRESSION TAG SEQRES 1 A 92 GLY PRO GLY SER GLU ASP LEU PRO LEU PRO PRO GLY TRP SEQRES 2 A 92 SER VAL ASP TRP THR MET ARG GLY ARG LYS TYR TYR ILE SEQRES 3 A 92 ASP HIS ASN THR ASN THR THR HIS TRP SER HIS PRO LEU SEQRES 4 A 92 GLU ARG GLU GLY LEU PRO PRO GLY TRP GLU ARG VAL GLU SEQRES 5 A 92 SER SER GLU PHE GLY THR TYR TYR VAL ASP HIS THR ASN SEQRES 6 A 92 LYS ARG ALA GLN TYR ARG HIS PRO CYS ALA PRO SER VAL SEQRES 7 A 92 PRO ARG TYR ASP GLN PRO PRO PRO ILE THR TYR GLN PRO SEQRES 8 A 92 GLN HET DIO A 301 6 HETNAM DIO 1,4-DIETHYLENE DIOXIDE FORMUL 2 DIO C4 H8 O2 FORMUL 3 HOH *66(H2 O) SHEET 1 AA1 3 TRP A 206 TRP A 210 0 SHEET 2 AA1 3 LYS A 216 ASP A 220 -1 O ILE A 219 N SER A 207 SHEET 3 AA1 3 THR A 225 HIS A 227 -1 O THR A 225 N ASP A 220 SHEET 1 AA2 3 TRP A 241 VAL A 244 0 SHEET 2 AA2 3 TYR A 252 ASP A 255 -1 O TYR A 252 N VAL A 244 SHEET 3 AA2 3 ARG A 260 GLN A 262 -1 O ARG A 260 N ASP A 255 SSBOND 1 CYS A 267 CYS A 267 1555 6555 2.02 SITE 1 AC1 4 SER A 247 GLU A 248 HIS A 265 ALA A 268 CRYST1 46.715 46.715 83.151 90.00 90.00 120.00 P 31 2 1 6 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 0.021406 0.012359 0.000000 0.00000 SCALE2 0.000000 0.024718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012026 0.00000