HEADER PROTEIN BINDING 04-OCT-22 8B82 TITLE CRYSTAL STRUCTURE OF SCRIBBLE PDZ1 WITH HUMAN PAPILLOMAVIRUS STRAIN 16 TITLE 2 E6 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SCRIBBLE HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SCRIBBLE,HSCRIB,PROTEIN LAP4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN E6; COMPND 8 CHAIN: C, D; COMPND 9 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: HUMAN PAPILLOMAVIRUS TYPE 18; SOURCE 12 ORGANISM_TAXID: 333761 KEYWDS SCRIBBLE, HUMAN PAPILLOMAVIRUS, E6, PDZ DOMAIN, CELL POLARITY, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.Z.STEWART,M.KVANSAKUL REVDAT 1 18-OCT-23 8B82 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. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 5671 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 289 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 49.7400 - 3.5300 0.98 2731 155 0.2320 0.2646 REMARK 3 2 3.5300 - 2.8000 0.99 2651 134 0.2636 0.3112 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) : 0.349 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.31 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 1792 REMARK 3 ANGLE : 0.471 2408 REMARK 3 CHIRALITY : 0.045 267 REMARK 3 PLANARITY : 0.005 328 REMARK 3 DIHEDRAL : 14.449 689 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): -13.3072 17.2103 -15.7530 REMARK 3 T TENSOR REMARK 3 T11: 0.4168 T22: 0.7141 REMARK 3 T33: 0.0256 T12: -0.0367 REMARK 3 T13: -0.1006 T23: 0.0625 REMARK 3 L TENSOR REMARK 3 L11: 0.2234 L22: 1.4077 REMARK 3 L33: 0.1780 L12: -0.0500 REMARK 3 L13: -0.1457 L23: -0.0574 REMARK 3 S TENSOR REMARK 3 S11: -0.0116 S12: 0.1082 S13: 0.0254 REMARK 3 S21: 0.3135 S22: -0.0473 S23: -0.0893 REMARK 3 S31: -0.0819 S32: -0.1126 S33: -0.0351 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 8B82 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 : 5671 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 49.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.13810 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52390 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: ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 0.05 M AMMONIUM SULFATE, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.20500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.14200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.62650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.14200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.20500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.62650 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 ALA B 701 REMARK 465 PRO B 702 REMARK 465 SER B 703 REMARK 465 VAL B 704 REMARK 465 LYS B 705 REMARK 465 GLY B 706 REMARK 465 VAL B 707 REMARK 465 SER B 708 REMARK 465 PHE B 709 REMARK 465 ARG C 149 REMARK 465 LEU C 150 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 ASN A 713 CG OD1 ND2 REMARK 470 THR A 735 OG1 CG2 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 ARG A 815 -71.37 -77.93 REMARK 500 GLU B 766 -136.78 53.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1025 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH B1029 DISTANCE = 7.20 ANGSTROMS DBREF 8B82 A 701 816 UNP Q14160 SCRIB_HUMAN 701 816 DBREF 8B82 B 701 816 UNP Q14160 SCRIB_HUMAN 701 816 DBREF 8B82 C 149 158 UNP P06463 VE6_HPV18 149 158 DBREF 8B82 D 149 158 UNP P06463 VE6_HPV18 149 158 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 B 116 ALA PRO SER VAL LYS GLY VAL SER PHE ASP GLN ALA ASN SEQRES 2 B 116 ASN LEU LEU ILE GLU PRO ALA ARG ILE GLU GLU GLU GLU SEQRES 3 B 116 LEU THR LEU THR ILE LEU ARG GLN THR GLY GLY LEU GLY SEQRES 4 B 116 ILE SER ILE ALA GLY GLY LYS GLY SER THR PRO TYR LYS SEQRES 5 B 116 GLY ASP ASP GLU GLY ILE PHE ILE SER ARG VAL SER GLU SEQRES 6 B 116 GLU GLY PRO ALA ALA ARG ALA GLY VAL ARG VAL GLY ASP SEQRES 7 B 116 LYS LEU LEU GLU VAL ASN GLY VAL ALA LEU GLN GLY ALA SEQRES 8 B 116 GLU HIS HIS GLU ALA VAL GLU ALA LEU ARG GLY ALA GLY SEQRES 9 B 116 THR ALA VAL GLN MET ARG VAL TRP ARG GLU ARG MET SEQRES 1 C 10 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL SEQRES 1 D 10 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL HET CL A 901 1 HET CL A 902 1 HET CL A 903 1 HET CL B 901 1 HETNAM CL CHLORIDE ION FORMUL 5 CL 4(CL 1-) FORMUL 9 HOH *66(H2 O) HELIX 1 AA1 GLY A 767 GLY A 773 1 7 HELIX 2 AA2 GLU A 792 GLY A 802 1 11 HELIX 3 AA3 GLU B 766 GLY B 773 1 8 HELIX 4 AA4 GLU B 792 GLY B 802 1 11 SHEET 1 AA1 2 ASP A 710 ALA A 712 0 SHEET 2 AA1 2 LEU A 715 ILE A 717 -1 O ILE A 717 N ASP A 710 SHEET 1 AA2 4 GLU A 724 LEU A 732 0 SHEET 2 AA2 4 ALA A 806 GLU A 814 -1 O VAL A 807 N ILE A 731 SHEET 3 AA2 4 LYS A 779 VAL A 783 -1 N LEU A 781 O ARG A 810 SHEET 4 AA2 4 VAL A 786 ALA A 787 -1 O VAL A 786 N VAL A 783 SHEET 1 AA3 3 PHE A 759 VAL A 763 0 SHEET 2 AA3 3 ILE A 740 ALA A 743 -1 N SER A 741 O SER A 761 SHEET 3 AA3 3 GLU D 155 GLN D 157 -1 O THR D 156 N ILE A 742 SHEET 1 AA4 4 GLU B 724 LEU B 732 0 SHEET 2 AA4 4 ALA B 806 GLU B 814 -1 O ARG B 813 N GLU B 725 SHEET 3 AA4 4 LYS B 779 VAL B 783 -1 N LEU B 781 O ARG B 810 SHEET 4 AA4 4 VAL B 786 ALA B 787 -1 O VAL B 786 N VAL B 783 SHEET 1 AA5 6 GLU B 724 LEU B 732 0 SHEET 2 AA5 6 ALA B 806 GLU B 814 -1 O ARG B 813 N GLU B 725 SHEET 3 AA5 6 LYS B 779 VAL B 783 -1 N LEU B 781 O ARG B 810 SHEET 4 AA5 6 ILE B 758 VAL B 763 -1 N ILE B 758 O LEU B 780 SHEET 5 AA5 6 ILE B 740 ALA B 743 -1 N SER B 741 O SER B 761 SHEET 6 AA5 6 GLU C 155 GLN C 157 -1 O THR C 156 N ILE B 742 CRYST1 34.410 55.253 114.284 90.00 90.00 90.00 P 21 21 21 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 0.029061 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008750 0.00000