HEADER PEPTIDE BINDING PROTEIN/PROTEIN BINDING 16-APR-13 4K72 TITLE CFTR ASSOCIATED LIGAND (CAL) PDZ DOMAIN BOUND TO PEPTIDE ICAL36-VQD TITLE 2 (ANSRVQDSII) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOLGI-ASSOCIATED PDZ AND COILED-COIL MOTIF-CONTAINING COMPND 3 PROTEIN; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: PDZ DOMAIN; COMPND 6 SYNONYM: CFTR-ASSOCIATED LIGAND, FUSED IN GLIOBLASTOMA, PDZ PROTEIN COMPND 7 INTERACTING SPECIFICALLY WITH TC10, PIST; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ICAL36-VQD PEPTIDE; COMPND 11 CHAIN: C, D; 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: GOPC, CAL, FIG; 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 DOMAIN, CAL, PIST, FIG, PDZ-PEPTIDE COMPLEX, CFTR ASSOCIATED KEYWDS 2 LIGAND, CFTR, PEPTIDE BINDING PROTEIN-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.F.AMACHER,D.R.MADDEN REVDAT 3 20-SEP-23 4K72 1 REMARK REVDAT 2 21-OCT-20 4K72 1 REMARK REVDAT 1 22-JAN-14 4K72 0 JRNL AUTH J.F.AMACHER,P.R.CUSHING,L.BROOKS,P.BOISGUERIN,D.R.MADDEN JRNL TITL STEREOCHEMICAL PREFERENCES MODULATE AFFINITY AND SELECTIVITY JRNL TITL 2 AMONG FIVE PDZ DOMAINS THAT BIND CFTR: COMPARATIVE JRNL TITL 3 STRUCTURAL AND SEQUENCE ANALYSES. JRNL REF STRUCTURE V. 22 82 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24210758 JRNL DOI 10.1016/J.STR.2013.09.019 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15162 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) : 0.179 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 763 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 19.5707 - 3.2450 1.00 2936 156 0.1699 0.1872 REMARK 3 2 3.2450 - 2.5775 1.00 2878 162 0.1775 0.2531 REMARK 3 3 2.5775 - 2.2523 1.00 2869 149 0.1830 0.2561 REMARK 3 4 2.2523 - 2.0466 1.00 2880 149 0.1792 0.2485 REMARK 3 5 2.0466 - 1.9000 0.99 2836 147 0.2077 0.2615 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 : 0.83 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 52.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.090 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) : 2.61960 REMARK 3 B22 (A**2) : 3.97010 REMARK 3 B33 (A**2) : -6.58960 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.85440 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 1444 REMARK 3 ANGLE : 1.096 1949 REMARK 3 CHIRALITY : 0.067 229 REMARK 3 PLANARITY : 0.005 256 REMARK 3 DIHEDRAL : 15.440 543 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 284:370 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4728 27.4083 40.0222 REMARK 3 T TENSOR REMARK 3 T11: 0.1135 T22: 0.1203 REMARK 3 T33: 0.1122 T12: -0.0030 REMARK 3 T13: -0.0037 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.5905 L22: 0.8266 REMARK 3 L33: 0.7055 L12: 0.0483 REMARK 3 L13: -0.4538 L23: 0.0606 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.0832 S13: 0.0138 REMARK 3 S21: 0.0517 S22: 0.0014 S23: 0.0153 REMARK 3 S31: -0.0937 S32: 0.0434 S33: -0.0084 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND RESID 284:370 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0841 29.3068 17.1063 REMARK 3 T TENSOR REMARK 3 T11: 0.1254 T22: 0.1066 REMARK 3 T33: 0.1333 T12: 0.0199 REMARK 3 T13: -0.0070 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 1.0008 L22: 0.5627 REMARK 3 L33: 0.9665 L12: 0.4209 REMARK 3 L13: -0.2435 L23: -0.4067 REMARK 3 S TENSOR REMARK 3 S11: 0.0367 S12: -0.0243 S13: -0.0316 REMARK 3 S21: -0.0380 S22: -0.0156 S23: 0.0089 REMARK 3 S31: 0.1301 S32: 0.1296 S33: -0.0239 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 4K72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-11 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 : 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) : 0.8856 REMARK 200 MONOCHROMATOR : S1 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 : 15168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 19.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.590 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 15.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51400 REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 FOR SHELL : 3.590 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 4E34 (CAL PDZ DOMAIN BOUND TO ICAL36 REMARK 200 PEPTIDE) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% (W/V) POLYETHYLENE GLYCOL (PEG) REMARK 280 1000, 0.1 M SODIUM THIOSULFATE PENTAHYDRATE, 0.1 M REMARK 280 TRIS(HYDROXYMETHYL)AMINOMETHANE (TRIS), PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.39550 REMARK 290 SMTRY3 2 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: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 C 1 REMARK 465 ASN C 2 REMARK 465 SER C 3 REMARK 465 ARG C 4 REMARK 465 VAL C 5 REMARK 465 GLN C 6 REMARK 465 ALA D 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K6Y RELATED DB: PDB REMARK 900 RELATED ID: 4K75 RELATED DB: PDB REMARK 900 RELATED ID: 4K76 RELATED DB: PDB REMARK 900 RELATED ID: 4K78 RELATED DB: PDB REMARK 900 RELATED ID: 4JOP RELATED DB: PDB REMARK 900 RELATED ID: 4JOR RELATED DB: PDB DBREF 4K72 A 284 370 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 4K72 B 284 370 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 4K72 C 1 10 PDB 4K72 4K72 1 10 DBREF 4K72 D 1 10 PDB 4K72 4K72 1 10 SEQRES 1 A 87 GLY PRO ILE ARG LYS VAL LEU LEU LEU LYS GLU ASP HIS SEQRES 2 A 87 GLU GLY LEU GLY ILE SER ILE THR GLY GLY LYS GLU HIS SEQRES 3 A 87 GLY VAL PRO ILE LEU ILE SER GLU ILE HIS PRO GLY GLN SEQRES 4 A 87 PRO ALA ASP ARG CYS GLY GLY LEU HIS VAL GLY ASP ALA SEQRES 5 A 87 ILE LEU ALA VAL ASN GLY VAL ASN LEU ARG ASP THR LYS SEQRES 6 A 87 HIS LYS GLU ALA VAL THR ILE LEU SER GLN GLN ARG GLY SEQRES 7 A 87 GLU ILE GLU PHE GLU VAL VAL TYR VAL SEQRES 1 B 87 GLY PRO ILE ARG LYS VAL LEU LEU LEU LYS GLU ASP HIS SEQRES 2 B 87 GLU GLY LEU GLY ILE SER ILE THR GLY GLY LYS GLU HIS SEQRES 3 B 87 GLY VAL PRO ILE LEU ILE SER GLU ILE HIS PRO GLY GLN SEQRES 4 B 87 PRO ALA ASP ARG CYS GLY GLY LEU HIS VAL GLY ASP ALA SEQRES 5 B 87 ILE LEU ALA VAL ASN GLY VAL ASN LEU ARG ASP THR LYS SEQRES 6 B 87 HIS LYS GLU ALA VAL THR ILE LEU SER GLN GLN ARG GLY SEQRES 7 B 87 GLU ILE GLU PHE GLU VAL VAL TYR VAL SEQRES 1 C 10 ALA ASN SER ARG VAL GLN ASP SER ILE ILE SEQRES 1 D 10 ALA ASN SER ARG VAL GLN ASP SER ILE ILE FORMUL 5 HOH *141(H2 O) HELIX 1 1 LYS A 307 GLY A 310 5 4 HELIX 2 2 GLN A 322 GLY A 328 1 7 HELIX 3 3 LYS A 348 GLN A 359 1 12 HELIX 4 4 LYS B 307 GLY B 310 5 4 HELIX 5 5 GLN B 322 GLY B 328 1 7 HELIX 6 6 LYS B 348 GLN B 359 1 12 SHEET 1 A 4 ARG A 287 LYS A 293 0 SHEET 2 A 4 GLY A 361 VAL A 368 -1 O PHE A 365 N VAL A 289 SHEET 3 A 4 ALA A 335 VAL A 339 -1 N ALA A 335 O VAL A 368 SHEET 4 A 4 VAL A 342 ASN A 343 -1 O VAL A 342 N VAL A 339 SHEET 1 B 6 ARG A 287 LYS A 293 0 SHEET 2 B 6 GLY A 361 VAL A 368 -1 O PHE A 365 N VAL A 289 SHEET 3 B 6 ALA A 335 VAL A 339 -1 N ALA A 335 O VAL A 368 SHEET 4 B 6 VAL A 311 ILE A 318 -1 N ILE A 313 O ILE A 336 SHEET 5 B 6 ILE A 301 GLY A 306 -1 N THR A 304 O LEU A 314 SHEET 6 B 6 SER C 8 ILE C 10 -1 O ILE C 10 N ILE A 301 SHEET 1 C 4 ARG B 287 LEU B 292 0 SHEET 2 C 4 GLU B 362 TYR B 369 -1 O ILE B 363 N LEU B 291 SHEET 3 C 4 ASP B 334 VAL B 339 -1 N ALA B 335 O VAL B 368 SHEET 4 C 4 VAL B 342 ASN B 343 -1 O VAL B 342 N VAL B 339 SHEET 1 D 3 VAL B 311 ILE B 318 0 SHEET 2 D 3 ILE B 301 GLY B 306 -1 N THR B 304 O LEU B 314 SHEET 3 D 3 ASP D 7 ILE D 10 -1 O ILE D 10 N ILE B 301 CRYST1 36.250 48.791 54.900 90.00 92.79 90.00 P 1 21 1 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 0.027586 0.000000 0.001343 0.00000 SCALE2 0.000000 0.020496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018237 0.00000