HEADER SIGNALING PROTEIN 27-FEB-19 6JJY TITLE CRYSTAL STRUCTURE OF KIBRA AND BETA-DYSTROGLYCAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN KIBRA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KIDNEY AND BRAIN PROTEIN,KIBRA,WW DOMAIN-CONTAINING PROTEIN COMPND 5 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPTIDE FROM DYSTROGLYCAN; COMPND 9 CHAIN: U; COMPND 10 SYNONYM: DYSTROPHIN-ASSOCIATED GLYCOPROTEIN 1; COMPND 11 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: WWC1, KIAA0869; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: DAG1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS WW TANDEM, PY TANDEM, KIBRA, PTPN14, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.LIN,Z.YANG,Z.JI,M.ZHANG REVDAT 2 22-NOV-23 6JJY 1 REMARK REVDAT 1 25-SEP-19 6JJY 0 JRNL AUTH Z.LIN,Z.YANG,R.XIE,Z.JI,K.GUAN,M.ZHANG JRNL TITL DECODING WW DOMAIN TANDEM-MEDIATED TARGET RECOGNITIONS IN JRNL TITL 2 TISSUE GROWTH AND CELL POLARITY. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31486770 JRNL DOI 10.7554/ELIFE.49439 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 14386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1439 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 40.5776 - 4.9473 0.98 1444 159 0.1683 0.2153 REMARK 3 2 4.9473 - 3.9278 0.99 1387 153 0.1590 0.1974 REMARK 3 3 3.9278 - 3.4316 0.99 1357 153 0.1814 0.2171 REMARK 3 4 3.4316 - 3.1180 0.99 1342 149 0.2201 0.3239 REMARK 3 5 3.1180 - 2.8946 0.98 1344 150 0.2487 0.2904 REMARK 3 6 2.8946 - 2.7240 0.96 1284 140 0.2665 0.3117 REMARK 3 7 2.7240 - 2.5876 0.93 1268 133 0.2482 0.2902 REMARK 3 8 2.5876 - 2.4750 0.91 1215 136 0.2448 0.2547 REMARK 3 9 2.4750 - 2.3797 0.88 1164 135 0.2528 0.2993 REMARK 3 10 2.3797 - 2.2976 0.86 1142 131 0.2772 0.3489 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.480 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 : 0.009 1249 REMARK 3 ANGLE : 1.101 1711 REMARK 3 CHIRALITY : 0.040 174 REMARK 3 PLANARITY : 0.006 229 REMARK 3 DIHEDRAL : 15.926 467 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): -94.2259 65.4788 127.1158 REMARK 3 T TENSOR REMARK 3 T11: 0.3127 T22: 0.2697 REMARK 3 T33: 0.3133 T12: 0.0122 REMARK 3 T13: 0.0522 T23: 0.0342 REMARK 3 L TENSOR REMARK 3 L11: 0.7193 L22: -0.0379 REMARK 3 L33: 2.6504 L12: 0.5142 REMARK 3 L13: -1.4105 L23: -0.6824 REMARK 3 S TENSOR REMARK 3 S11: -0.1048 S12: -0.0338 S13: 0.0505 REMARK 3 S21: 0.1623 S22: 0.0939 S23: 0.0559 REMARK 3 S31: 0.1397 S32: -0.1175 S33: 0.0396 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 6JJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.9791 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 : 15114 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.88600 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: 6J68 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0-4.0M NACL, 100MM BIS-TRIS (PH REMARK 280 6.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 0.00000 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 0.00000 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 0.00000 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 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: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U 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 S SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 O3 SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 S SO4 U 901 LIES ON A SPECIAL POSITION. REMARK 375 O1 SO4 U 901 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 HIS A 132 REMARK 465 GLY U 875 REMARK 465 PRO U 876 REMARK 465 GLY U 877 REMARK 465 SER U 878 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 PHE A 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 40 CD NE CZ NH1 NH2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ARG U 879 CG CD NE CZ NH1 NH2 REMARK 470 LYS U 881 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 U 901 DBREF 6JJY A 5 132 UNP Q5SXA9 KIBRA_MOUSE 5 132 DBREF 6JJY U 877 895 UNP Q14118 DAG1_HUMAN 877 895 SEQADV 6JJY GLY A -1 UNP Q5SXA9 EXPRESSION TAG SEQADV 6JJY PRO A 0 UNP Q5SXA9 EXPRESSION TAG SEQADV 6JJY GLY A 1 UNP Q5SXA9 EXPRESSION TAG SEQADV 6JJY SER A 2 UNP Q5SXA9 EXPRESSION TAG SEQADV 6JJY GLU A 3 UNP Q5SXA9 EXPRESSION TAG SEQADV 6JJY PHE A 4 UNP Q5SXA9 EXPRESSION TAG SEQADV 6JJY GLY U 875 UNP Q14118 EXPRESSION TAG SEQADV 6JJY PRO U 876 UNP Q14118 EXPRESSION TAG SEQRES 1 A 134 GLY PRO GLY SER GLU PHE GLU LEU PRO LEU PRO GLU GLY SEQRES 2 A 134 TRP GLU GLU ALA ARG ASP PHE ASP GLY LYS VAL TYR TYR SEQRES 3 A 134 ILE ASP HIS ARG ASN ARG THR THR SER TRP ILE ASP PRO SEQRES 4 A 134 ARG ASP ARG TYR THR LYS PRO LEU THR PHE ALA ASP CYS SEQRES 5 A 134 ILE SER ASP GLU LEU PRO LEU GLY TRP GLU GLU ALA TYR SEQRES 6 A 134 ASP PRO GLN VAL GLY ASP TYR PHE ILE ASP HIS ASN THR SEQRES 7 A 134 LYS THR THR GLN ILE GLU ASP PRO ARG VAL GLN TRP ARG SEQRES 8 A 134 ARG GLU GLN GLU HIS MET LEU LYS ASP TYR LEU VAL VAL SEQRES 9 A 134 ALA GLN GLU ALA LEU SER ALA GLN LYS GLU ILE TYR GLN SEQRES 10 A 134 VAL LYS GLN GLN ARG LEU GLU LEU ALA GLN GLN GLU TYR SEQRES 11 A 134 GLN GLN LEU HIS SEQRES 1 U 21 GLY PRO GLY SER ARG PRO LYS ASN MET THR PRO TYR ARG SEQRES 2 U 21 SER PRO PRO PRO TYR VAL PRO PRO HET SO4 A 201 5 HET SO4 U 901 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *75(H2 O) HELIX 1 AA1 ARG A 38 THR A 42 5 5 HELIX 2 AA2 THR A 46 CYS A 50 5 5 HELIX 3 AA3 ASP A 83 GLN A 129 1 47 SHEET 1 AA1 3 TRP A 12 ARG A 16 0 SHEET 2 AA1 3 VAL A 22 ASP A 26 -1 O ILE A 25 N GLU A 13 SHEET 3 AA1 3 THR A 31 SER A 33 -1 O SER A 33 N TYR A 24 SHEET 1 AA2 3 TRP A 59 ASP A 64 0 SHEET 2 AA2 3 GLY A 68 ASP A 73 -1 O GLY A 68 N ASP A 64 SHEET 3 AA2 3 THR A 78 GLN A 80 -1 O THR A 78 N ASP A 73 CISPEP 1 ILE A 51 SER A 52 0 -2.30 SITE 1 AC1 3 PRO U 891 TYR U 892 VAL U 893 CRYST1 73.483 73.483 105.322 90.00 90.00 120.00 P 3 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 0.013609 0.007857 0.000000 0.00000 SCALE2 0.000000 0.015714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009495 0.00000