HEADER PEPTIDE BINDING PROTEIN 07-MAY-19 6OV7 TITLE CFTR ASSOCIATED LIGAND (CAL) PDZ DOMAIN BOUND TO PEPTIDE KCAL01 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 SYNONYM: CFTR-ASSOCIATED LIGAND,FUSED IN GLIOBLASTOMA,PDZ PROTEIN COMPND 6 INTERACTING SPECIFICALLY WITH TC10,PIST; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: KCAL01 PEPTIDE; COMPND 10 CHAIN: C, 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: GOPC, CAL, FIG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET16B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 OTHER_DETAILS: ENGINEERED KEYWDS PDZ DOMAIN, INHIBITOR, COMPLEX, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.P.GILL,D.R.MADDEN REVDAT 4 11-OCT-23 6OV7 1 REMARK REVDAT 3 25-DEC-19 6OV7 1 JRNL REVDAT 2 27-NOV-19 6OV7 1 JRNL REVDAT 1 20-NOV-19 6OV7 0 JRNL AUTH G.T.HOLT,J.D.JOU,N.P.GILL,A.U.LOWEGARD,J.W.MARTIN, JRNL AUTH 2 D.R.MADDEN,B.R.DONALD JRNL TITL COMPUTATIONAL ANALYSIS OF ENERGY LANDSCAPES REVEALS DYNAMIC JRNL TITL 2 FEATURES THAT CONTRIBUTE TO BINDING OF INHIBITORS TO JRNL TITL 3 CFTR-ASSOCIATED LIGAND. JRNL REF J.PHYS.CHEM.B V. 123 10441 2019 JRNL REFN ISSN 1089-5647 JRNL PMID 31697075 JRNL DOI 10.1021/ACS.JPCB.9B07278 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX VERSION 1.14-3260-000 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1160 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 38.4240 - 3.4261 0.99 2961 0 0.1683 0.2049 REMARK 3 2 3.4261 - 2.7196 1.00 2890 0 0.1721 0.1872 REMARK 3 3 2.7196 - 2.3759 1.00 2817 0 0.1742 0.2056 REMARK 3 4 2.3759 - 2.1587 1.00 2823 0 0.1753 0.2141 REMARK 3 5 2.1587 - 2.0040 1.00 2766 0 0.1736 0.1987 REMARK 3 6 2.0040 - 1.8858 1.00 2814 0 0.2024 0.2577 REMARK 3 7 1.8858 - 1.7914 1.00 2769 0 0.2364 0.2686 REMARK 3 8 1.7914 - 1.7134 0.96 2681 0 0.2813 0.3067 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.56 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): 12.4682 27.6297 30.5801 REMARK 3 T TENSOR REMARK 3 T11: 0.0457 T22: 0.0449 REMARK 3 T33: 0.0428 T12: -0.0014 REMARK 3 T13: 0.0021 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.1922 L22: 0.1574 REMARK 3 L33: 0.3094 L12: -0.1687 REMARK 3 L13: 0.1997 L23: -0.2453 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: 0.0340 S13: -0.0143 REMARK 3 S21: 0.0161 S22: 0.0198 S23: -0.0060 REMARK 3 S31: -0.0220 S32: -0.0072 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ALPHA HELIX-1 OF CHAIN B APPEARS REMARK 3 DISTORTED DUE TO DISULFIDE FORMATION. CHAIN A RETAINS NORMAL REMARK 3 ALPHA HELICAL STRUCTURE. REMARK 4 REMARK 4 6OV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) AND SI(220) DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION NOVEMBER 1, 2016 REMARK 200 DATA SCALING SOFTWARE : XSCALE VERSION NOVEMBER 1, 2016 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27416 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.460 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 8.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 9.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.37 REMARK 200 R MERGE FOR SHELL (I) : 0.95900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 49.99 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX PHASER-MR VERSION 1.14-3260-000 REMARK 200 STARTING MODEL: 4E34 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 MG/ML CAL PDZ, 1 MM KCAL01 PEPTIDE, REMARK 280 25% (W/V) PEG 8000, 5% PEG 400, 150 MM NACL, AND 100 MM TRIS PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, 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 21.81100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.58200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.38350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.58200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.81100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.38350 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: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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: 1020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5410 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 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 ALA D 1 REMARK 465 ASN D 2 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 352 -98.57 -110.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 6OV7 A 276 362 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 6OV7 B 276 362 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 6OV7 C 1 10 PDB 6OV7 6OV7 1 10 DBREF 6OV7 D 1 10 PDB 6OV7 6OV7 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 TRP GLN VAL THR ARG VAL SEQRES 1 D 10 ALA ASN SER ARG TRP GLN VAL THR ARG VAL FORMUL 5 HOH *175(H2 O) HELIX 1 AA1 LYS A 299 GLY A 302 5 4 HELIX 2 AA2 GLN A 314 GLY A 320 1 7 HELIX 3 AA3 LYS A 340 GLN A 350 1 11 HELIX 4 AA4 LYS B 299 GLY B 302 5 4 HELIX 5 AA5 LYS B 340 GLN B 350 1 11 SHEET 1 AA1 4 ARG A 279 LEU A 284 0 SHEET 2 AA1 4 GLU A 354 TYR A 361 -1 O PHE A 357 N VAL A 281 SHEET 3 AA1 4 ASP A 326 VAL A 331 -1 N ALA A 327 O VAL A 360 SHEET 4 AA1 4 VAL A 334 ASN A 335 -1 O VAL A 334 N VAL A 331 SHEET 1 AA2 3 VAL A 303 ILE A 310 0 SHEET 2 AA2 3 ILE A 293 GLY A 298 -1 N THR A 296 O LEU A 306 SHEET 3 AA2 3 VAL C 7 VAL C 10 -1 O VAL C 10 N ILE A 293 SHEET 1 AA3 4 ARG B 279 LYS B 285 0 SHEET 2 AA3 4 GLY B 353 TYR B 361 -1 O ILE B 355 N LEU B 283 SHEET 3 AA3 4 ASP B 326 VAL B 331 -1 N ALA B 327 O VAL B 360 SHEET 4 AA3 4 VAL B 334 ASN B 335 -1 O VAL B 334 N VAL B 331 SHEET 1 AA4 3 VAL B 303 ILE B 310 0 SHEET 2 AA4 3 ILE B 293 GLY B 298 -1 N THR B 296 O LEU B 306 SHEET 3 AA4 3 VAL D 7 VAL D 10 -1 O VAL D 10 N ILE B 293 SSBOND 1 CYS A 319 CYS B 319 1555 1555 2.05 CRYST1 43.622 60.767 81.164 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 0.022924 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012321 0.00000