HEADER PROTEIN BINDING 02-NOV-22 8BIA TITLE CRYSTAL STRUCTURE OF SCRIBBLE PDZ1 WITH PTHR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SCRIBBLE HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SCRIBBLE,HSCRIB,PROTEIN LAP4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PARATHYROID HORMONE/PARATHYROID HORMONE-RELATED PEPTIDE COMPND 8 RECEPTOR; COMPND 9 CHAIN: C; COMPND 10 SYNONYM: PTH/PTHRP TYPE I RECEPTOR,PTH/PTHR RECEPTOR,PARATHYROID COMPND 11 HORMONE 1 RECEPTOR,PTH1 RECEPTOR; COMPND 12 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: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CODON+; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS SCRIBBLE, PTHR, PDZ DOMAIN, CELL POLARITY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.Z.STEWART,M.KVANSAKUL REVDAT 2 04-MAR-26 8BIA 1 REMARK REVDAT 1 15-NOV-23 8BIA 0 JRNL AUTH B.Z.STEWART,S.CARIA,P.O.HUMBERT,M.KVANSAKUL JRNL TITL CRYSTAL STRUCTURE OF SCRIBBLE PDZ1 WITH HUMAN PAPILLOMAVIRUS JRNL TITL 2 STRAIN 16 E6 PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 6456 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 334 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 51.6300 - 3.0200 0.99 3160 168 0.2427 0.2507 REMARK 3 2 3.0200 - 2.4000 0.98 2962 166 0.2922 0.3527 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.175 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.062 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.28 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 : 0.002 843 REMARK 3 ANGLE : 0.468 1137 REMARK 3 CHIRALITY : 0.046 127 REMARK 3 PLANARITY : 0.003 151 REMARK 3 DIHEDRAL : 15.396 314 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): 15.0246 27.1692 -12.4513 REMARK 3 T TENSOR REMARK 3 T11: 0.2301 T22: 0.6505 REMARK 3 T33: 0.3182 T12: -0.0640 REMARK 3 T13: -0.0488 T23: 0.0416 REMARK 3 L TENSOR REMARK 3 L11: 2.7634 L22: 3.1619 REMARK 3 L33: 4.4389 L12: -0.3216 REMARK 3 L13: -0.5340 L23: 0.3540 REMARK 3 S TENSOR REMARK 3 S11: 0.1516 S12: -0.4933 S13: 0.0803 REMARK 3 S21: 0.3607 S22: -0.1271 S23: -0.3808 REMARK 3 S31: -0.3155 S32: 0.3712 S33: -0.0815 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 8BIA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-22 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6472 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 51.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6MTV REMARK 200 REMARK 200 REMARK: TRIANGULAR DIAMOND PRISM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE/CITRATE PH 5.2, 43% REMARK 280 PEG 300, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 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,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 26.58050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 26.58050 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 108.50500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.25250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.58050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 162.75750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 162.75750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.58050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.25250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 26.58050 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 108.50500 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 26.58050 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 108.50500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 26.58050 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 162.75750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 54.25250 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 26.58050 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 54.25250 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 162.75750 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 26.58050 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 26.58050 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 108.50500 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: 1220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 ALA A 701 REMARK 465 PRO A 702 REMARK 465 SER A 703 REMARK 465 VAL A 704 REMARK 465 LYS A 705 REMARK 465 GLY A 706 REMARK 465 VAL A 707 REMARK 465 SER A 708 REMARK 465 PHE A 709 REMARK 465 ASP A 710 REMARK 465 GLN A 711 REMARK 465 ALA A 712 REMARK 465 ASN A 713 REMARK 465 ASN A 714 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 ARG A 721 CG CD NE CZ NH1 NH2 DBREF 8BIA A 701 816 UNP Q14160 SCRIB_HUMAN 701 816 DBREF 8BIA C 464 471 UNP Q03431 PTH1R_HUMAN 586 593 SEQRES 1 A 116 ALA PRO SER VAL LYS GLY VAL SER PHE ASP GLN ALA ASN SEQRES 2 A 116 ASN LEU LEU ILE GLU PRO ALA ARG ILE GLU GLU GLU GLU SEQRES 3 A 116 LEU THR LEU THR ILE LEU ARG GLN THR GLY GLY LEU GLY SEQRES 4 A 116 ILE SER ILE ALA GLY GLY LYS GLY SER THR PRO TYR LYS SEQRES 5 A 116 GLY ASP ASP GLU GLY ILE PHE ILE SER ARG VAL SER GLU SEQRES 6 A 116 GLU GLY PRO ALA ALA ARG ALA GLY VAL ARG VAL GLY ASP SEQRES 7 A 116 LYS LEU LEU GLU VAL ASN GLY VAL ALA LEU GLN GLY ALA SEQRES 8 A 116 GLU HIS HIS GLU ALA VAL GLU ALA LEU ARG GLY ALA GLY SEQRES 9 A 116 THR ALA VAL GLN MET ARG VAL TRP ARG GLU ARG MET SEQRES 1 C 8 GLN GLU GLU TRP GLU THR VAL MET HET PO4 C 501 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *35(H2 O) HELIX 1 AA1 GLY A 767 ALA A 772 1 6 HELIX 2 AA2 GLU A 792 GLY A 802 1 11 SHEET 1 AA1 4 GLU A 724 LEU A 732 0 SHEET 2 AA1 4 ALA A 806 GLU A 814 -1 O MET A 809 N LEU A 729 SHEET 3 AA1 4 LYS A 779 VAL A 783 -1 N LEU A 781 O ARG A 810 SHEET 4 AA1 4 VAL A 786 ALA A 787 -1 O VAL A 786 N VAL A 783 SHEET 1 AA2 6 GLU A 724 LEU A 732 0 SHEET 2 AA2 6 ALA A 806 GLU A 814 -1 O MET A 809 N LEU A 729 SHEET 3 AA2 6 LYS A 779 VAL A 783 -1 N LEU A 781 O ARG A 810 SHEET 4 AA2 6 ILE A 758 VAL A 763 -1 N ILE A 758 O LEU A 780 SHEET 5 AA2 6 ILE A 740 ALA A 743 -1 N SER A 741 O SER A 761 SHEET 6 AA2 6 THR C 469 VAL C 470 -1 O THR C 469 N ILE A 742 CRYST1 53.161 53.161 217.010 90.00 90.00 90.00 I 41 2 2 16 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 0.018811 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004608 0.00000 CONECT 1653 1654 1655 1656 1657 CONECT 1654 1653 CONECT 1655 1653 CONECT 1656 1653 CONECT 1657 1653 MASTER 284 0 1 2 10 0 0 6 870 2 5 10 END