HEADER PROTEIN BINDING 24-SEP-14 4REX TITLE CRYSTAL STRUCTURE OF THE FIRST WW DOMAIN OF HUMAN YAP2 ISOFORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: YORKIE HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WW DOMAIN (UNP RESIDUES 165-209); COMPND 5 SYNONYM: 65 KDA YES-ASSOCIATED PROTEIN, YAP65; COMPND 6 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: YAP1, YAP65; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM30 KEYWDS WW DOMAIN, HIPPO SIGNALING PATHWAY, ANTIPARALLEL BETA-SHEET, PROTEIN KEYWDS 2 BINDING, PROLINE RICH MOTIFS EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 4 20-SEP-23 4REX 1 REMARK SEQADV REVDAT 3 16-SEP-15 4REX 1 JRNL REVDAT 2 26-AUG-15 4REX 1 JRNL REVDAT 1 19-AUG-15 4REX 0 JRNL AUTH S.MARTINEZ-RODRIGUEZ,J.BACARIZO,I.LUQUE,A.CAMARA-ARTIGAS JRNL TITL CRYSTAL STRUCTURE OF THE FIRST WW DOMAIN OF HUMAN YAP2 JRNL TITL 2 ISOFORM. JRNL REF J.STRUCT.BIOL. V. 191 381 2015 JRNL REFN ISSN 1047-8477 JRNL PMID 26256245 JRNL DOI 10.1016/J.JSB.2015.08.001 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 9891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 REMARK 3 FREE R VALUE TEST SET COUNT : 452 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 21.5524 - 2.3076 0.99 3174 165 0.1651 0.1846 REMARK 3 2 2.3076 - 1.8319 0.98 3114 139 0.1911 0.1898 REMARK 3 3 1.8319 - 1.6004 0.99 3151 148 0.1999 0.2408 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.70 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 : 0.011 401 REMARK 3 ANGLE : 1.356 547 REMARK 3 CHIRALITY : 0.056 56 REMARK 3 PLANARITY : 0.009 71 REMARK 3 DIHEDRAL : 14.606 145 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7509 51.9551 50.5746 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.1284 REMARK 3 T33: 0.1077 T12: -0.0164 REMARK 3 T13: 0.0038 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.2256 L22: 0.0384 REMARK 3 L33: 0.0829 L12: -0.0626 REMARK 3 L13: 0.0782 L23: -0.0534 REMARK 3 S TENSOR REMARK 3 S11: 0.0401 S12: -0.0047 S13: 0.1443 REMARK 3 S21: 0.0929 S22: 0.0185 S23: 0.0463 REMARK 3 S31: -0.0430 S32: 0.0772 S33: -0.0121 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 176 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9340 39.6485 49.5999 REMARK 3 T TENSOR REMARK 3 T11: 0.1026 T22: 0.1192 REMARK 3 T33: 0.1025 T12: 0.0110 REMARK 3 T13: 0.0122 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.0521 L22: 0.0985 REMARK 3 L33: 0.0347 L12: 0.0406 REMARK 3 L13: 0.0393 L23: 0.0517 REMARK 3 S TENSOR REMARK 3 S11: 0.1376 S12: 0.0665 S13: -0.0393 REMARK 3 S21: -0.0387 S22: -0.0089 S23: -0.0714 REMARK 3 S31: -0.0571 S32: 0.0320 S33: 0.0302 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 201 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5521 39.9777 52.2023 REMARK 3 T TENSOR REMARK 3 T11: 0.0750 T22: 0.0883 REMARK 3 T33: 0.0884 T12: -0.0069 REMARK 3 T13: 0.0002 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.0758 L22: 0.4625 REMARK 3 L33: 0.0905 L12: 0.0792 REMARK 3 L13: 0.0004 L23: 0.1416 REMARK 3 S TENSOR REMARK 3 S11: -0.0372 S12: 0.0258 S13: -0.0209 REMARK 3 S21: -0.0823 S22: 0.0523 S23: 0.1167 REMARK 3 S31: 0.0408 S32: -0.0419 S33: -0.0064 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 202 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7935 53.9910 52.7601 REMARK 3 T TENSOR REMARK 3 T11: 0.1525 T22: 0.1156 REMARK 3 T33: 0.1974 T12: -0.0304 REMARK 3 T13: -0.0012 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.0851 L22: 0.0996 REMARK 3 L33: 0.4114 L12: -0.0709 REMARK 3 L13: 0.1757 L23: -0.0990 REMARK 3 S TENSOR REMARK 3 S11: 0.1252 S12: 0.1232 S13: 0.1760 REMARK 3 S21: 0.0296 S22: 0.1133 S23: 0.1164 REMARK 3 S31: -0.0236 S32: 0.1420 S33: 0.0510 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 4REX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97926 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : SI(111) CHANNEL-CUT CRYSTAL REMARK 200 MONOCHROMATOR AND A PAIR OF KB REMARK 200 MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.13, AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5514 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : 0.10400 REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.58200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 2HO2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULPHATE, 0.1 M SODIUM REMARK 280 ACETATE, 100 MM PROLINE, 5 MM NDSB-201 AND 5MM MBCD, PH 5.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 21.33650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.55050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.33650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.55050 REMARK 290 SMTRY3 4 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 420 LIES ON A SPECIAL POSITION. 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 GLN A 209 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 301 DBREF 4REX A 165 209 UNP P46937 YAP1_HUMAN 165 209 SEQADV 4REX GLY A 161 UNP P46937 EXPRESSION TAG SEQADV 4REX ALA A 162 UNP P46937 EXPRESSION TAG SEQADV 4REX MET A 163 UNP P46937 EXPRESSION TAG SEQADV 4REX GLY A 164 UNP P46937 EXPRESSION TAG SEQRES 1 A 49 GLY ALA MET GLY PHE GLU ILE PRO ASP ASP VAL PRO LEU SEQRES 2 A 49 PRO ALA GLY TRP GLU MET ALA LYS THR SER SER GLY GLN SEQRES 3 A 49 ARG TYR PHE LEU ASN HIS ILE ASP GLN THR THR THR TRP SEQRES 4 A 49 GLN ASP PRO ARG LYS ALA MET LEU SER GLN HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *42(H2 O) HELIX 1 1 ASP A 201 LEU A 207 5 7 SHEET 1 A 3 TRP A 177 LYS A 181 0 SHEET 2 A 3 ARG A 187 ASN A 191 -1 O LEU A 190 N GLU A 178 SHEET 3 A 3 THR A 196 THR A 198 -1 O THR A 196 N ASN A 191 SITE 1 AC1 5 GLY A 161 GLY A 164 PHE A 165 GLU A 166 SITE 2 AC1 5 HOH A 417 CRYST1 42.673 43.101 21.302 90.00 90.00 90.00 P 21 21 2 4 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 0.023434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023201 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046944 0.00000