HEADER PEPTIDE BINDING PROTEIN/PROTEIN BINDING 16-APR-13 4K78
TITLE CFTR ASSOCIATED LIGAND (CAL) E317A PDZ DOMAIN BOUND TO PEPTIDE ICAL36-
TITLE 2 QDTRL (ANSRWQDTRL)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: GOLGI-ASSOCIATED PDZ AND COILED-COIL MOTIF-CONTAINING
COMPND 3 PROTEIN;
COMPND 4 CHAIN: A;
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 MUTATION: YES;
COMPND 10 MOL_ID: 2;
COMPND 11 MOLECULE: ICAL36-QDTRL PEPTIDE;
COMPND 12 CHAIN: B;
COMPND 13 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 2 20-SEP-23 4K78 1 SEQADV LINK
REVDAT 1 22-JAN-14 4K78 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. 1.80 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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.13
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 10780
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) : 0.183
REMARK 3 FREE R VALUE : 0.221
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190
REMARK 3 FREE R VALUE TEST SET COUNT : 560
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 19.1345 - 2.8550 1.00 2717 140 0.2022 0.2263
REMARK 3 2 2.8550 - 2.2672 1.00 2529 140 0.1766 0.2145
REMARK 3 3 2.2672 - 1.9810 1.00 2499 140 0.1516 0.2204
REMARK 3 4 1.9810 - 1.8000 1.00 2475 140 0.1741 0.2145
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 : 0.50
REMARK 3 B_SOL : 59.83
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.020
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) : 1.19690
REMARK 3 B22 (A**2) : 1.19690
REMARK 3 B33 (A**2) : -2.39390
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 : 0.008 786
REMARK 3 ANGLE : 1.203 1066
REMARK 3 CHIRALITY : 0.086 120
REMARK 3 PLANARITY : 0.005 142
REMARK 3 DIHEDRAL : 15.776 293
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN A AND RESID 284:370
REMARK 3 ORIGIN FOR THE GROUP (A): 10.5397 23.4476 36.7985
REMARK 3 T TENSOR
REMARK 3 T11: 0.0537 T22: 0.0563
REMARK 3 T33: 0.0549 T12: -0.0020
REMARK 3 T13: -0.0156 T23: 0.0106
REMARK 3 L TENSOR
REMARK 3 L11: 0.2044 L22: 0.4489
REMARK 3 L33: 0.4009 L12: -0.1454
REMARK 3 L13: 0.0330 L23: -0.1586
REMARK 3 S TENSOR
REMARK 3 S11: 0.0284 S12: -0.0587 S13: -0.0692
REMARK 3 S21: 0.0330 S22: 0.0204 S23: -0.0612
REMARK 3 S31: 0.0709 S32: 0.0063 S33: -0.0006
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 4K78 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_1000078978.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-APR-13
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) : 0.9795
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 : 10781
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 19.133
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.530
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.11000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.0100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 61.7000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.530
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 BOUND TO ICAL36 PEPTIDE)
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.38
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 40% (W/V) POLYETHYLENE GLYCOL (PEG),
REMARK 280 0.9 M SODIUM THIOSULFATE PENTAHYDRATE, 0.1 M TRIS(HYDROXYMETHYL)
REMARK 280 AMINOMETHANE (TRIS), PH 8.0, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/2
REMARK 290 6555 X-Y,X,Z+1/2
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z
REMARK 290 10555 -Y,-X,-Z+1/2
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+1/2
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.72300
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.72300
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.72300
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 48.72300
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 48.72300
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 48.72300
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: 1110 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: 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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 407 LIES ON A SPECIAL POSITION.
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4K6Y RELATED DB: PDB
REMARK 900 RELATED ID: 4K72 RELATED DB: PDB
REMARK 900 RELATED ID: 4K75 RELATED DB: PDB
REMARK 900 RELATED ID: 4K76 RELATED DB: PDB
DBREF 4K78 A 284 370 UNP Q9HD26 GOPC_HUMAN 284 370
DBREF 4K78 B 1 10 PDB 4K78 4K78 1 10
SEQADV 4K78 ALA A 317 UNP Q9HD26 GLU 317 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 ALA ILE HIS PRO GLY GLN
SEQRES 4 A 87 PRO ALA ASP ARG CSU 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 10 ALA ASN SER ARG TRP GLN ASP THR ARG LEU
MODRES 4K78 CSU A 327 CYS CYSTEINE-S-SULFONIC ACID
HET CSU A 327 10
HETNAM CSU CYSTEINE-S-SULFONIC ACID
FORMUL 1 CSU C3 H7 N O5 S2
FORMUL 3 HOH *69(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 358 1 11
SHEET 1 A 4 ARG A 287 LEU A 292 0
SHEET 2 A 4 GLU A 362 TYR A 369 -1 O ILE A 363 N LEU A 291
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 ASP B 7 LEU B 10 -1 O LEU B 10 N ILE A 301
LINK C ARG A 326 N CSU A 327 1555 1555 1.33
LINK C CSU A 327 N GLY A 328 1555 1555 1.33
CRYST1 61.821 61.821 97.446 90.00 90.00 120.00 P 63 2 2 12
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 0.016176 0.009339 0.000000 0.00000
SCALE2 0.000000 0.018678 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010262 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
