HEADER PROTEIN BINDING 04-JAN-14 4OAJ TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN SAP97 PDZ2 AND 5HT2A RECEPTOR TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ 2 DOMAIN; COMPND 5 SYNONYM: EMBRYO-DLG/SYNAPSE-ASSOCIATED PROTEIN 97, E-DLG/SAP97, COMPND 6 SYNAPSE-ASSOCIATED PROTEIN 97, SAP-97, SAP97; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5-HYDROXYTRYPTAMINE RECEPTOR 2A PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 465-471; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DLG1, DLGH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 11 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 12 ORGANISM_TAXID: 10116 KEYWDS PDZ DOMAIN, 5HT2A RECEPTOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.PANDALANENI,L.DORR,O.MAYANS,L.-Y.LIAN REVDAT 3 28-FEB-24 4OAJ 1 SEQADV REVDAT 2 24-JAN-18 4OAJ 1 AUTHOR JRNL REVDAT 1 29-JAN-14 4OAJ 0 JRNL AUTH S.PANDALANENI,L.DORR,O.MAYANS,L.-Y.LIAN JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN SAP97 PDZ2 AND JRNL TITL 2 5HT2A RECEPTOR PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 4904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 253 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 2.8974 - 2.3000 1.00 2255 135 0.2356 0.3299 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.23 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 : 0.008 738 REMARK 3 ANGLE : 1.103 994 REMARK 3 CHIRALITY : 0.071 120 REMARK 3 PLANARITY : 0.004 126 REMARK 3 DIHEDRAL : 16.477 271 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 315:406 ) OR ( CHAIN B AND RESID REMARK 3 14:20 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3859 14.3691 13.2993 REMARK 3 T TENSOR REMARK 3 T11: 0.3355 T22: 0.8133 REMARK 3 T33: 0.4718 T12: -0.0366 REMARK 3 T13: -0.0221 T23: -0.0856 REMARK 3 L TENSOR REMARK 3 L11: 1.3895 L22: 4.8822 REMARK 3 L33: 8.3340 L12: -1.8835 REMARK 3 L13: -1.1660 L23: -1.7440 REMARK 3 S TENSOR REMARK 3 S11: 0.2556 S12: 0.4573 S13: 0.0716 REMARK 3 S21: -0.2641 S22: -0.3492 S23: -0.0484 REMARK 3 S31: 0.3872 S32: 0.0979 S33: 0.0768 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 4OAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.970000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.189 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.850 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 17.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.64 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.65500 REMARK 200 FOR SHELL : 3.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M AMMONIUM SULFATE, 0.1M CITRIC REMARK 280 ACID PH4.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 58.74000 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 29.37000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.37000 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 58.74000 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: 850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5790 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 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 52.00 -158.12 REMARK 500 ASN A 375 -118.72 44.71 REMARK 500 SER A 395 107.37 -161.89 REMARK 500 ASP A 396 -64.32 69.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 4OAJ A 317 406 UNP Q811D0 DLG1_MOUSE 317 406 DBREF 4OAJ B 14 20 UNP P14842 5HT2A_RAT 465 471 SEQADV 4OAJ ALA A 315 UNP Q811D0 EXPRESSION TAG SEQADV 4OAJ ALA A 316 UNP Q811D0 EXPRESSION TAG SEQRES 1 A 92 ALA ALA ILE MET GLU ILE LYS LEU ILE LYS GLY PRO LYS SEQRES 2 A 92 GLY LEU GLY PHE SER ILE ALA GLY GLY VAL GLY ASN GLN SEQRES 3 A 92 HIS ILE PRO GLY ASP ASN SER ILE TYR VAL THR LYS ILE SEQRES 4 A 92 ILE GLU GLY GLY ALA ALA HIS LYS ASP GLY LYS LEU GLN SEQRES 5 A 92 ILE GLY ASP LYS LEU LEU ALA VAL ASN SER VAL CYS LEU SEQRES 6 A 92 GLU GLU VAL THR HIS GLU GLU ALA VAL THR ALA LEU LYS SEQRES 7 A 92 ASN THR SER ASP PHE VAL TYR LEU LYS VAL ALA LYS PRO SEQRES 8 A 92 THR SEQRES 1 B 7 ASN GLU LYS VAL SER CYS VAL FORMUL 3 HOH *14(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 ILE A 317 ILE A 323 0 SHEET 2 A 4 PHE A 397 ALA A 403 -1 O VAL A 402 N MET A 318 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 ILE A 317 ILE A 323 0 SHEET 2 B 6 PHE A 397 ALA A 403 -1 O VAL A 402 N MET A 318 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 SER B 18 VAL B 20 -1 O SER B 18 N ILE A 333 CRYST1 45.000 45.000 88.110 90.00 90.00 120.00 P 32 2 1 6 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 0.022222 0.012830 0.000000 0.00000 SCALE2 0.000000 0.025660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011349 0.00000