HEADER MEMBRANE PROTEIN/SIGNALING PROTEIN 18-JUL-12 4G69 TITLE STRUCTURE OF THE HUMAN DISCS LARGE 1 PDZ2 - ADENOMATOUS POLYPOSIS COLI TITLE 2 CYTOSKELETAL POLARITY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ2, UNP RESIDUES 310-407; COMPND 5 SYNONYM: SYNAPSE-ASSOCIATED PROTEIN 97, SAP-97, SAP97, HDLG; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ADENOMATOUS POLYPOSIS COLI PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: APC C-TERMINAL PEPTIDE, UNP RESIDUES 2833-2843; COMPND 11 SYNONYM: PROTEIN APC, DELETED IN POLYPOSIS 2.5; 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: DLG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: ADENOMATOUS POLYPOSIS COLI (APC) C-TERMINAL 11 SOURCE 17 RESIDUES SYNTHESIZED WITH N-TERMINAL TETRAMETHYL RHODAMINE TAG KEYWDS PDZ, MAGUK, POLARITY, ADENOMATOUS POLYPOSIS COLI, KEYWDS 2 TETRAMETHYLRHODAMINE, ADHERENS JUNCTION, MEMBRANE PROTEIN-SIGNALING KEYWDS 3 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP REVDAT 2 15-NOV-17 4G69 1 REMARK REVDAT 1 12-DEC-12 4G69 0 JRNL AUTH K.C.SLEP JRNL TITL STRUCTURE OF THE HUMAN DISCS LARGE 1 PDZ2- ADENOMATOUS JRNL TITL 2 POLYPOSIS COLI CYTOSKELETAL POLARITY COMPLEX: INSIGHT INTO JRNL TITL 3 PEPTIDE ENGAGEMENT AND PDZ CLUSTERING. JRNL REF PLOS ONE V. 7 50097 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23185543 JRNL DOI 10.1371/JOURNAL.PONE.0050097 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 6846 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 688 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 29.3823 - 3.4146 0.99 1351 151 0.1676 0.1678 REMARK 3 2 3.4146 - 2.7108 0.98 1277 143 0.1763 0.1821 REMARK 3 3 2.7108 - 2.3683 0.97 1255 139 0.1782 0.1913 REMARK 3 4 2.3683 - 2.1519 0.96 1208 139 0.1651 0.2035 REMARK 3 5 2.1519 - 1.9977 0.85 1067 116 0.1640 0.1872 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 32.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.050 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) : -2.88850 REMARK 3 B22 (A**2) : 0.33000 REMARK 3 B33 (A**2) : 2.55860 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 : 0.007 779 REMARK 3 ANGLE : 0.980 1051 REMARK 3 CHIRALITY : 0.063 127 REMARK 3 PLANARITY : 0.004 132 REMARK 3 DIHEDRAL : 12.794 288 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): -4.1675 -4.9337 14.8774 REMARK 3 T TENSOR REMARK 3 T11: 0.0144 T22: 0.0142 REMARK 3 T33: 0.0138 T12: -0.0003 REMARK 3 T13: 0.0033 T23: -0.0293 REMARK 3 L TENSOR REMARK 3 L11: 0.4398 L22: 0.3595 REMARK 3 L33: 0.2922 L12: 0.0187 REMARK 3 L13: 0.2044 L23: -0.2575 REMARK 3 S TENSOR REMARK 3 S11: 0.0080 S12: 0.0054 S13: -0.0127 REMARK 3 S21: -0.0022 S22: -0.0015 S23: -0.0104 REMARK 3 S31: 0.0030 S32: -0.0302 S33: 0.0062 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 4G69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 REMARK 200 MONOCHROMATOR : COLLECTED AT 1.127 A REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6846 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.22000 REMARK 200 FOR SHELL : 4.800 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 2FE5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 1.4 MM DLG1 PDZ2, REMARK 280 1.7 MM APC, 100 MM NACL, 25 MM TRIS PH 7.0, 0.1% B-ME WELL: 200 REMARK 280 MM SODIUM ACETATE, 100 MM SODIUM CACODYLATE PH 6.25, 28% PEG REMARK 280 8000 DROP = 1:1 PROTEIN:WELL SOLUTION , VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 300K 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 13.55450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.87800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.59200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.87800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.55450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.59200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 GLY A 308 REMARK 465 SER A 309 REMARK 465 SER A 407 REMARK 465 ARG B 2833 REMARK 465 HIS B 2834 REMARK 465 SER B 2835 REMARK 465 GLY B 2836 REMARK 465 SER B 2837 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 310 CG CD NE CZ NH1 NH2 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 A 553 O HOH A 602 2.08 REMARK 500 O HOH A 534 O HOH A 560 2.10 REMARK 500 O HOH A 558 O HOH A 579 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 339 39.65 -153.33 REMARK 500 ASN A 375 -116.96 52.29 REMARK 500 ASN A 393 54.81 -90.89 REMARK 500 SER A 395 -155.71 -92.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 4G69 A 310 407 UNP Q12959 DLG1_HUMAN 310 407 DBREF 4G69 B 2833 2843 UNP P25054 APC_HUMAN 2833 2843 SEQADV 4G69 GLY A 308 UNP Q12959 EXPRESSION TAG SEQADV 4G69 SER A 309 UNP Q12959 EXPRESSION TAG SEQRES 1 A 100 GLY SER ARG LYS PRO VAL SER GLU LYS ILE MET GLU ILE SEQRES 2 A 100 LYS LEU ILE LYS GLY PRO LYS GLY LEU GLY PHE SER ILE SEQRES 3 A 100 ALA GLY GLY VAL GLY ASN GLN HIS ILE PRO GLY ASP ASN SEQRES 4 A 100 SER ILE TYR VAL THR LYS ILE ILE GLU GLY GLY ALA ALA SEQRES 5 A 100 HIS LYS ASP GLY LYS LEU GLN ILE GLY ASP LYS LEU LEU SEQRES 6 A 100 ALA VAL ASN ASN VAL CYS LEU GLU GLU VAL THR HIS GLU SEQRES 7 A 100 GLU ALA VAL THR ALA LEU LYS ASN THR SER ASP PHE VAL SEQRES 8 A 100 TYR LEU LYS VAL ALA LYS PRO THR SER SEQRES 1 B 11 ARG HIS SER GLY SER TYR LEU VAL THR SER VAL FORMUL 3 HOH *106(H2 O) HELIX 1 1 GLY A 357 GLY A 363 1 7 HELIX 2 2 THR A 383 ASN A 393 1 11 SHEET 1 A 4 GLU A 315 ILE A 323 0 SHEET 2 A 4 PHE A 397 PRO A 405 -1 O LEU A 400 N ILE A 320 SHEET 3 A 4 LYS A 370 VAL A 374 -1 N LEU A 372 O LYS A 401 SHEET 4 A 4 VAL A 377 CYS A 378 -1 O VAL A 377 N VAL A 374 SHEET 1 B 6 GLU A 315 ILE A 323 0 SHEET 2 B 6 PHE A 397 PRO A 405 -1 O LEU A 400 N ILE A 320 SHEET 3 B 6 LYS A 370 VAL A 374 -1 N LEU A 372 O LYS A 401 SHEET 4 B 6 ILE A 348 ILE A 353 -1 N ILE A 348 O LEU A 371 SHEET 5 B 6 PHE A 331 GLY A 335 -1 N ALA A 334 O TYR A 349 SHEET 6 B 6 THR B2841 SER B2842 -1 O THR B2841 N ILE A 333 CRYST1 27.109 51.184 71.756 90.00 90.00 90.00 P 21 21 21 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 0.036888 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019537 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013936 0.00000 MASTER 269 0 0 2 10 0 0 6 0 0 0 9 END