HEADER PEPTIDE BINDING PROTEIN 20-MAY-16 5K4F TITLE CAL PDZ MUTANT C319A WITH A PEPTIDE 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: UNP RESIDUES 284-370; COMPND 6 SYNONYM: CFTR-ASSOCIATED LIGAND,FUSED IN GLIOBLASTOMA,PDZ PROTEIN COMPND 7 INTERACTING SPECIFICALLY WITH TC10,PIST; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HPV18E6 PEPTIDE; COMPND 12 CHAIN: C, D; COMPND 13 FRAGMENT: UNP RESIDUES 149-158; COMPND 14 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); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HUMAN PAPILLOMAVIRUS TYPE 18; SOURCE 12 ORGANISM_TAXID: 333761 KEYWDS CAL PDZ MUTANT, C319A, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,D.R.MADDEN REVDAT 5 27-SEP-23 5K4F 1 REMARK REVDAT 4 25-DEC-19 5K4F 1 REMARK REVDAT 3 22-NOV-17 5K4F 1 REMARK REVDAT 2 13-SEP-17 5K4F 1 REMARK REVDAT 1 09-AUG-17 5K4F 0 JRNL AUTH Y.ZHAO,D.R.MADDEN JRNL TITL CAL PDZ DOMAIN MUTANT WITH A PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 33527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1700 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 18.7928 - 3.1094 0.95 2597 170 0.1583 0.1656 REMARK 3 2 3.1094 - 2.4698 1.00 2738 85 0.1614 0.1791 REMARK 3 3 2.4698 - 2.1581 1.00 2625 170 0.1488 0.1898 REMARK 3 4 2.1581 - 1.9610 1.00 2652 170 0.1353 0.1870 REMARK 3 5 1.9610 - 1.8206 1.00 2696 85 0.1395 0.1674 REMARK 3 6 1.8206 - 1.7133 1.00 2643 170 0.1392 0.2045 REMARK 3 7 1.7133 - 1.6275 1.00 2624 170 0.1425 0.1814 REMARK 3 8 1.6275 - 1.5567 1.00 2720 85 0.1447 0.1989 REMARK 3 9 1.5567 - 1.4968 0.99 2610 170 0.1539 0.1985 REMARK 3 10 1.4968 - 1.4452 0.99 2643 170 0.1673 0.2410 REMARK 3 11 1.4452 - 1.4000 0.99 2701 85 0.1847 0.2381 REMARK 3 12 1.4000 - 1.3600 0.99 2578 170 0.2113 0.2554 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.840 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) : 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 : 0.006 1646 REMARK 3 ANGLE : 0.879 2254 REMARK 3 CHIRALITY : 0.077 253 REMARK 3 PLANARITY : 0.007 314 REMARK 3 DIHEDRAL : 19.214 643 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 5K4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221442. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-16 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 : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS 20151015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33527 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 18.791 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.260 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.26 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.090 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: 4E34 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 31% PEG3350, 125MM NACL, 0.1M TRIS7.5, REMARK 280 PH 7.5, VAPOR DIFFUSION, 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 24.13800 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 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 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 ARG C -3 REMARK 465 LEU C -2 REMARK 465 GLN C -1 REMARK 465 ARG C 0 REMARK 465 ARG D -5 REMARK 465 LEU D -4 REMARK 465 GLN D -3 REMARK 465 ARG D -2 REMARK 465 ARG D -1 REMARK 465 ARG D 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 444 O HOH B 450 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 5K4F A 276 362 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 5K4F C -3 6 UNP P06463 VE6_HPV18 149 158 DBREF 5K4F B 276 362 UNP Q9HD26 GOPC_HUMAN 284 370 DBREF 5K4F D -5 4 UNP P06463 VE6_HPV18 149 158 SEQADV 5K4F ALA A 319 UNP Q9HD26 CYS 327 ENGINEERED MUTATION SEQADV 5K4F ALA B 319 UNP Q9HD26 CYS 327 ENGINEERED MUTATION 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 ALA 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 C 10 ARG LEU GLN ARG ARG ARG GLU THR GLN 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 ALA 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 D 10 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL FORMUL 5 HOH *143(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 351 1 12 HELIX 4 AA4 LYS B 299 GLY B 302 5 4 HELIX 5 AA5 GLN B 314 GLY B 320 1 7 HELIX 6 AA6 LYS B 340 GLN B 351 1 12 SHEET 1 AA1 4 ARG A 279 LEU A 284 0 SHEET 2 AA1 4 GLU A 354 TYR A 361 -1 O ILE A 355 N LEU A 283 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 SER A 294 O SER A 308 SHEET 3 AA2 3 GLU C 3 VAL C 6 -1 O VAL C 6 N ILE A 293 SHEET 1 AA3 4 ARG B 279 LEU B 284 0 SHEET 2 AA3 4 GLU B 354 TYR B 361 -1 O PHE B 357 N VAL B 281 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 THR D 2 VAL D 4 -1 O VAL D 4 N ILE B 293 CRYST1 32.730 48.276 51.435 90.00 101.76 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 0.030553 0.000000 0.006359 0.00000 SCALE2 0.000000 0.020714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019859 0.00000