HEADER SIGNALING PROTEIN/INHIBITOR 13-JUN-11 3SFJ TITLE CRYSTAL STRUCTURE OF TAX-INTERACTING PROTEIN-1 (TIP-1) PDZ DOMAIN TITLE 2 BOUND TO ICAL36 INHIBITOR PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAX1-BINDING PROTEIN 3; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PDZ DOMAIN (UNP RESIDUES 10-112); COMPND 5 SYNONYM: TAX-INTERACTING PROTEIN-1, TIP-1, GLUTAMINASE-INTERACTING COMPND 6 PROTEIN 3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DECAMERIC PEPTIDE ICAL36; COMPND 10 CHAIN: B, D; COMPND 11 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: TAX1BP3, TIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PDZ:PEPTIDE COMPLEX, SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.F.AMACHER,D.R.MADDEN REVDAT 2 13-SEP-23 3SFJ 1 SEQADV REVDAT 1 12-DEC-12 3SFJ 0 JRNL AUTH P.R.CUSHING,L.VOUILLEME,J.F.AMACHER,P.BOISGUERIN,D.R.MADDEN JRNL TITL A CAL INHIBITOR WITH SINGLE-PDZ SPECIFICITY RESCUES JRNL TITL 2 DELTAF508-CFTR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 60547 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 3044 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 19.1099 - 3.4679 0.98 2795 162 0.1709 0.1558 REMARK 3 2 3.4679 - 2.7552 0.98 2786 170 0.1710 0.1893 REMARK 3 3 2.7552 - 2.4077 0.97 2753 169 0.1834 0.1953 REMARK 3 4 2.4077 - 2.1879 0.97 2794 128 0.1719 0.1866 REMARK 3 5 2.1879 - 2.0313 0.97 2790 116 0.1773 0.2132 REMARK 3 6 2.0313 - 1.9116 0.96 2727 142 0.1694 0.1922 REMARK 3 7 1.9116 - 1.8160 0.96 2757 150 0.1745 0.2008 REMARK 3 8 1.8160 - 1.7370 0.96 2739 156 0.1716 0.1800 REMARK 3 9 1.7370 - 1.6701 0.95 2700 147 0.1685 0.1876 REMARK 3 10 1.6701 - 1.6125 0.95 2741 136 0.1730 0.2030 REMARK 3 11 1.6125 - 1.5621 0.95 2721 140 0.1833 0.2197 REMARK 3 12 1.5621 - 1.5175 0.94 2692 148 0.1817 0.2443 REMARK 3 13 1.5175 - 1.4776 0.94 2706 142 0.1879 0.2118 REMARK 3 14 1.4776 - 1.4415 0.94 2678 136 0.1967 0.2099 REMARK 3 15 1.4415 - 1.4088 0.94 2683 141 0.2099 0.2348 REMARK 3 16 1.4088 - 1.3788 0.93 2717 141 0.2042 0.2355 REMARK 3 17 1.3788 - 1.3512 0.93 2614 136 0.2050 0.2384 REMARK 3 18 1.3512 - 1.3257 0.93 2711 144 0.2221 0.2485 REMARK 3 19 1.3257 - 1.3021 0.92 2627 144 0.2349 0.2405 REMARK 3 20 1.3021 - 1.2800 0.81 2259 110 0.2266 0.2468 REMARK 3 21 1.2800 - 1.2594 0.67 1959 101 0.2492 0.2204 REMARK 3 22 1.2594 - 1.2400 0.55 1546 85 0.2718 0.2569 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 : 0.40 REMARK 3 B_SOL : 44.91 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.580 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) : -4.60020 REMARK 3 B22 (A**2) : 8.89100 REMARK 3 B33 (A**2) : -4.29080 REMARK 3 B12 (A**2) : 0.41860 REMARK 3 B13 (A**2) : -0.16520 REMARK 3 B23 (A**2) : 1.76330 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 : 0.006 1961 REMARK 3 ANGLE : 1.011 2660 REMARK 3 CHIRALITY : 0.070 290 REMARK 3 PLANARITY : 0.004 357 REMARK 3 DIHEDRAL : 13.365 766 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3SFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 65.687 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 27.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43900 REMARK 200 R SYM FOR SHELL (I) : 0.27100 REMARK 200 FOR SHELL : 4.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3DIW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% W/V PEG1000, 0.1 M AMMONIUM REMARK 280 THIOCYANATE, 0.1 M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 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: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 VAL A 10 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 TRP B 5 85.22 -154.15 REMARK 500 TRP D 5 87.26 -151.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 3SFJ A 11 113 UNP O14907 TX1B3_HUMAN 10 112 DBREF 3SFJ C 11 113 UNP O14907 TX1B3_HUMAN 10 112 DBREF 3SFJ B 1 10 PDB 3SFJ 3SFJ 1 10 DBREF 3SFJ D 1 10 PDB 3SFJ 3SFJ 1 10 SEQADV 3SFJ VAL A 10 UNP O14907 EXPRESSION TAG SEQADV 3SFJ VAL C 10 UNP O14907 EXPRESSION TAG SEQRES 1 A 104 VAL THR ALA VAL VAL GLN ARG VAL GLU ILE HIS LYS LEU SEQRES 2 A 104 ARG GLN GLY GLU ASN LEU ILE LEU GLY PHE SER ILE GLY SEQRES 3 A 104 GLY GLY ILE ASP GLN ASP PRO SER GLN ASN PRO PHE SER SEQRES 4 A 104 GLU ASP LYS THR ASP LYS GLY ILE TYR VAL THR ARG VAL SEQRES 5 A 104 SER GLU GLY GLY PRO ALA GLU ILE ALA GLY LEU GLN ILE SEQRES 6 A 104 GLY ASP LYS ILE MET GLN VAL ASN GLY TRP ASP MET THR SEQRES 7 A 104 MET VAL THR HIS ASP GLN ALA ARG LYS ARG LEU THR LYS SEQRES 8 A 104 ARG SER GLU GLU VAL VAL ARG LEU LEU VAL THR ARG GLN SEQRES 1 B 10 ALA ASN SER ARG TRP PRO THR SER ILE ILE SEQRES 1 C 104 VAL THR ALA VAL VAL GLN ARG VAL GLU ILE HIS LYS LEU SEQRES 2 C 104 ARG GLN GLY GLU ASN LEU ILE LEU GLY PHE SER ILE GLY SEQRES 3 C 104 GLY GLY ILE ASP GLN ASP PRO SER GLN ASN PRO PHE SER SEQRES 4 C 104 GLU ASP LYS THR ASP LYS GLY ILE TYR VAL THR ARG VAL SEQRES 5 C 104 SER GLU GLY GLY PRO ALA GLU ILE ALA GLY LEU GLN ILE SEQRES 6 C 104 GLY ASP LYS ILE MET GLN VAL ASN GLY TRP ASP MET THR SEQRES 7 C 104 MET VAL THR HIS ASP GLN ALA ARG LYS ARG LEU THR LYS SEQRES 8 C 104 ARG SER GLU GLU VAL VAL ARG LEU LEU VAL THR ARG GLN SEQRES 1 D 10 ALA ASN SER ARG TRP PRO THR SER ILE ILE FORMUL 5 HOH *256(H2 O) HELIX 1 1 ASP A 41 ASN A 45 5 5 HELIX 2 2 GLY A 65 GLY A 71 1 7 HELIX 3 3 THR A 90 THR A 99 1 10 HELIX 4 4 ASP C 41 ASN C 45 5 5 HELIX 5 5 GLY C 65 GLY C 71 1 7 HELIX 6 6 THR C 90 THR C 99 1 10 SHEET 1 A 4 VAL A 13 HIS A 20 0 SHEET 2 A 4 VAL A 105 ARG A 112 -1 O VAL A 106 N ILE A 19 SHEET 3 A 4 LYS A 77 VAL A 81 -1 N MET A 79 O LEU A 109 SHEET 4 A 4 TRP A 84 ASP A 85 -1 O TRP A 84 N VAL A 81 SHEET 1 B 6 VAL A 13 HIS A 20 0 SHEET 2 B 6 VAL A 105 ARG A 112 -1 O VAL A 106 N ILE A 19 SHEET 3 B 6 LYS A 77 VAL A 81 -1 N MET A 79 O LEU A 109 SHEET 4 B 6 ILE A 56 VAL A 61 -1 N ILE A 56 O ILE A 78 SHEET 5 B 6 PHE A 32 GLY A 36 -1 N GLY A 35 O TYR A 57 SHEET 6 B 6 THR B 7 ILE B 10 -1 O ILE B 10 N PHE A 32 SHEET 1 C 2 LEU A 22 GLN A 24 0 SHEET 2 C 2 ASN A 27 ILE A 29 -1 O ILE A 29 N LEU A 22 SHEET 1 D 4 VAL C 13 HIS C 20 0 SHEET 2 D 4 VAL C 105 ARG C 112 -1 O VAL C 106 N ILE C 19 SHEET 3 D 4 LYS C 77 VAL C 81 -1 N MET C 79 O LEU C 109 SHEET 4 D 4 TRP C 84 ASP C 85 -1 O TRP C 84 N VAL C 81 SHEET 1 E 6 VAL C 13 HIS C 20 0 SHEET 2 E 6 VAL C 105 ARG C 112 -1 O VAL C 106 N ILE C 19 SHEET 3 E 6 LYS C 77 VAL C 81 -1 N MET C 79 O LEU C 109 SHEET 4 E 6 ILE C 56 VAL C 61 -1 N ILE C 56 O ILE C 78 SHEET 5 E 6 PHE C 32 GLY C 36 -1 N GLY C 35 O TYR C 57 SHEET 6 E 6 THR D 7 ILE D 10 -1 O ILE D 10 N PHE C 32 SHEET 1 F 2 LEU C 22 GLN C 24 0 SHEET 2 F 2 ASN C 27 ILE C 29 -1 O ASN C 27 N GLN C 24 CRYST1 26.970 34.088 66.861 79.64 87.15 89.97 P 1 2 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 0.037078 -0.000019 -0.001873 0.00000 SCALE2 0.000000 0.029336 -0.005369 0.00000 SCALE3 0.000000 0.000000 0.015224 0.00000