HEADER PEPTIDE BINDING PROTEIN 18-MAR-13 4JOE TITLE CFTR ASSOCIATED LIGAND (CAL) PDZ DOMAIN BOUND TO PEPTIDE A-ICAL36 TITLE 2 (ANSRAPTSII) 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: CAL PDZ DOMAIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: A-ICAL36 PEPTIDE; COMPND 9 CHAIN: C, D; COMPND 10 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, CFTR ASSOCIATED LIGAND, CAL, FIG, PIST, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.F.AMACHER,D.R.MADDEN REVDAT 2 20-SEP-23 4JOE 1 REMARK REVDAT 1 22-JAN-14 4JOE 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. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 63011 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3144 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 18.5332 - 2.4558 0.95 6035 300 0.1950 0.1811 REMARK 3 2 2.4558 - 1.9499 1.00 6098 316 0.1734 0.1916 REMARK 3 3 1.9499 - 1.7036 1.00 6052 316 0.1644 0.1918 REMARK 3 4 1.7036 - 1.5480 1.00 5999 316 0.1584 0.1983 REMARK 3 5 1.5480 - 1.4371 1.00 5983 316 0.1619 0.1824 REMARK 3 6 1.4371 - 1.3524 1.00 5966 316 0.1690 0.1922 REMARK 3 7 1.3524 - 1.2846 1.00 5964 316 0.1805 0.1988 REMARK 3 8 1.2846 - 1.2287 1.00 5947 316 0.1947 0.2095 REMARK 3 9 1.2287 - 1.1814 1.00 5907 316 0.2071 0.2061 REMARK 3 10 1.1814 - 1.1400 1.00 5916 316 0.2351 0.2296 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.40 REMARK 3 SHRINKAGE RADIUS : 0.04 REMARK 3 K_SOL : 0.53 REMARK 3 B_SOL : 71.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.780 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) : 2.29410 REMARK 3 B22 (A**2) : -1.11520 REMARK 3 B33 (A**2) : -1.17890 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.005 1543 REMARK 3 ANGLE : 1.077 2090 REMARK 3 CHIRALITY : 0.067 241 REMARK 3 PLANARITY : 0.006 278 REMARK 3 DIHEDRAL : 13.946 587 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): 22.1346 28.4281 34.7262 REMARK 3 T TENSOR REMARK 3 T11: 0.0404 T22: 0.0458 REMARK 3 T33: 0.0523 T12: -0.0011 REMARK 3 T13: 0.0013 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.4859 L22: 0.8124 REMARK 3 L33: 0.8186 L12: -0.3479 REMARK 3 L13: -0.0658 L23: 0.1039 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: -0.0328 S13: -0.0242 REMARK 3 S21: 0.0345 S22: 0.0130 S23: -0.0136 REMARK 3 S31: 0.0156 S32: 0.0163 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B AND RESID 284:370 REMARK 3 ORIGIN FOR THE GROUP (A): 25.8961 26.7739 10.4696 REMARK 3 T TENSOR REMARK 3 T11: 0.0778 T22: 0.0480 REMARK 3 T33: 0.0439 T12: 0.0052 REMARK 3 T13: 0.0054 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.5099 L22: 1.2630 REMARK 3 L33: 1.3219 L12: -0.1786 REMARK 3 L13: -0.5259 L23: 0.6301 REMARK 3 S TENSOR REMARK 3 S11: 0.0637 S12: 0.0268 S13: 0.0338 REMARK 3 S21: -0.2083 S22: -0.0257 S23: 0.0190 REMARK 3 S31: -0.1843 S32: 0.0104 S33: -0.0242 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 4JOE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078300. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : 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 : 63014 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 18.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.990 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : 0.11600 REMARK 200 FOR THE DATA SET : 10.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : 0.39300 REMARK 200 FOR SHELL : 3.990 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 (%): 40.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31% (W/V) POLYETHYLENE GLYCOL (PEG) REMARK 280 3350, 0.05 M SODIUM CHLORIDE, 0.1 M TRIS(HYDROXYMETHYL) REMARK 280 AMINOMETHANE (TRIS), PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 18.33950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.83250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.90800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.83250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.33950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.90800 REMARK 290 SMTRY3 4 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: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JOF RELATED DB: PDB REMARK 900 RELATED ID: 4JOG RELATED DB: PDB REMARK 900 RELATED ID: 4JOH RELATED DB: PDB REMARK 900 RELATED ID: 4JOJ RELATED DB: PDB REMARK 900 RELATED ID: 4JOK RELATED DB: PDB REMARK 900 RELATED ID: 4JOP RELATED DB: PDB REMARK 900 RELATED ID: 4JOR RELATED DB: PDB DBREF 4JOE A 284 370 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 4JOE B 284 370 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 4JOE C 1 10 PDB 4JOE 4JOE 1 10 DBREF 4JOE D 1 10 PDB 4JOE 4JOE 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 ALA PRO THR SER ILE ILE SEQRES 1 D 10 ALA ASN SER ARG ALA PRO THR SER ILE ILE HET GOL A 401 6 HET GOL A 402 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *235(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 LEU A 292 0 SHEET 2 A 4 GLU A 362 TYR A 369 -1 O PHE A 365 N VAL A 289 SHEET 3 A 4 ASP A 334 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 3 VAL A 311 ILE A 318 0 SHEET 2 B 3 ILE A 301 GLY A 306 -1 N THR A 304 O LEU A 314 SHEET 3 B 3 THR C 7 ILE C 10 -1 O ILE C 10 N ILE A 301 SHEET 1 C 4 ARG B 287 LYS B 293 0 SHEET 2 C 4 GLY B 361 VAL B 368 -1 O PHE B 365 N VAL B 289 SHEET 3 C 4 ALA B 335 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 SER D 8 ILE D 10 -1 O SER D 8 N ILE B 303 SITE 1 AC1 9 ASP A 295 ASP A 346 LYS A 348 GLU A 351 SITE 2 AC1 9 HOH A 601 LYS B 288 LEU B 290 GLU B 364 SITE 3 AC1 9 HOH B 481 SITE 1 AC2 9 LEU A 292 LYS A 293 GLU A 294 LYS A 350 SITE 2 AC2 9 GLY A 361 GLU A 362 HOH A 507 HOH A 518 SITE 3 AC2 9 HOH B 490 CRYST1 36.679 47.816 97.665 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 0.027263 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020914 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010239 0.00000