HEADER SIGNALING PROTEIN 24-JAN-19 6QJK TITLE CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN OF PSD-95 PROTEIN D332G TITLE 2 MUTANT: SPACE GROUP P43 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 SYNONYM: POSTSYNAPTIC DENSITY PROTEIN 95,PSD-95,SYNAPSE-ASSOCIATED COMPND 6 PROTEIN 90,SAP90; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DLG4, PSD95; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS PDZ DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 3 24-JAN-24 6QJK 1 REMARK REVDAT 2 24-APR-19 6QJK 1 JRNL REVDAT 1 17-APR-19 6QJK 0 SPRSDE 17-APR-19 6QJK 5OIH JRNL AUTH A.CAMARA-ARTIGAS,J.MURCIANO-CALLES,J.C.MARTINEZ JRNL TITL CONFORMATIONAL CHANGES IN THE THIRD PDZ DOMAIN OF THE JRNL TITL 2 NEURONAL POSTSYNAPTIC DENSITY PROTEIN 95. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 381 2019 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 30988255 JRNL DOI 10.1107/S2059798319001980 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 75143 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 3591 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 19.4934 - 3.0952 0.98 2824 161 0.1409 0.1363 REMARK 3 2 3.0952 - 2.4583 0.98 2825 139 0.1457 0.1467 REMARK 3 3 2.4583 - 2.1480 0.99 2886 94 0.1319 0.1325 REMARK 3 4 2.1480 - 1.9518 0.96 2777 122 0.1357 0.1300 REMARK 3 5 1.9518 - 1.8120 0.97 2786 145 0.1260 0.1540 REMARK 3 6 1.8120 - 1.7053 0.97 2860 116 0.1254 0.1401 REMARK 3 7 1.7053 - 1.6199 0.97 2778 166 0.1231 0.1323 REMARK 3 8 1.6199 - 1.5494 0.97 2762 146 0.1216 0.1323 REMARK 3 9 1.5494 - 1.4898 0.96 2809 163 0.1216 0.1405 REMARK 3 10 1.4898 - 1.4384 0.96 2796 114 0.1190 0.1302 REMARK 3 11 1.4384 - 1.3934 0.97 2753 128 0.1264 0.1302 REMARK 3 12 1.3934 - 1.3536 0.96 2744 195 0.1257 0.1488 REMARK 3 13 1.3536 - 1.3180 0.96 2797 114 0.1285 0.1399 REMARK 3 14 1.3180 - 1.2858 0.96 2726 158 0.1271 0.1337 REMARK 3 15 1.2858 - 1.2566 0.95 2710 156 0.1306 0.1698 REMARK 3 16 1.2566 - 1.2299 0.95 2778 142 0.1376 0.1529 REMARK 3 17 1.2299 - 1.2053 0.94 2695 132 0.1455 0.1688 REMARK 3 18 1.2053 - 1.1825 0.94 2763 108 0.1352 0.1182 REMARK 3 19 1.1825 - 1.1614 0.94 2645 162 0.1438 0.1727 REMARK 3 20 1.1614 - 1.1417 0.95 2787 120 0.1470 0.1710 REMARK 3 21 1.1417 - 1.1233 0.94 2671 150 0.1528 0.1936 REMARK 3 22 1.1233 - 1.1060 0.93 2649 186 0.1689 0.1746 REMARK 3 23 1.1060 - 1.0898 0.94 2661 152 0.1772 0.2038 REMARK 3 24 1.0898 - 1.0744 0.92 2667 98 0.1924 0.2147 REMARK 3 25 1.0744 - 1.0599 0.93 2781 124 0.2059 0.1728 REMARK 3 26 1.0599 - 1.0461 0.92 2622 100 0.2215 0.2831 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.11 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 : 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 6QJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-14 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : CHANNEL-CUT DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (CINEL), REMARK 200 CRYOCOOLED, 6MM GAP REMARK 200 OPTICS : SAMPLE-DETECTOR DISTANCE: REMARK 200 ADJUSTABLE 123-1356MM REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.6 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 19.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3K82 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M AMMONIUM SULPHATE , 25.5% PEG REMARK 280 8000 , 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.45450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.18175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.72725 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLU A 305 REMARK 465 LYS A 403 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 363 -123.95 52.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OIH RELATED DB: PDB REMARK 900 5OIH CONTAINS THE SAME PROTEIN WITH THOSE SIDE CHAINS WITH POOR REMARK 900 ELECTRON DENSITY TRUNCATED AT CB DBREF 6QJK A 305 403 UNP P78352 DLG4_HUMAN 348 446 SEQADV 6QJK GLY A 332 UNP P78352 ASP 375 ENGINEERED MUTATION SEQRES 1 A 99 GLU ASP ILE PRO ARG GLU PRO ARG ARG ILE VAL ILE HIS SEQRES 2 A 99 ARG GLY SER THR GLY LEU GLY PHE ASN ILE VAL GLY GLY SEQRES 3 A 99 GLU GLY GLY GLU GLY ILE PHE ILE SER PHE ILE LEU ALA SEQRES 4 A 99 GLY GLY PRO ALA ASP LEU SER GLY GLU LEU ARG LYS GLY SEQRES 5 A 99 ASP GLN ILE LEU SER VAL ASN GLY VAL ASP LEU ARG ASN SEQRES 6 A 99 ALA SER HIS GLU GLN ALA ALA ILE ALA LEU LYS ASN ALA SEQRES 7 A 99 GLY GLN THR VAL THR ILE ILE ALA GLN TYR LYS PRO GLU SEQRES 8 A 99 GLU TYR SER ARG PHE GLU ALA LYS HET SO4 A 501 5 HET GOL A 502 9 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 O4 S 2- FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *104(H2 O) HELIX 1 AA1 GLY A 345 GLY A 351 1 7 HELIX 2 AA2 SER A 371 ASN A 381 1 11 HELIX 3 AA3 LYS A 393 ALA A 402 1 10 SHEET 1 AA1 4 ARG A 312 HIS A 317 0 SHEET 2 AA1 4 THR A 385 TYR A 392 -1 O ILE A 388 N ILE A 314 SHEET 3 AA1 4 ASP A 357 VAL A 362 -1 N GLN A 358 O GLN A 391 SHEET 4 AA1 4 VAL A 365 ASP A 366 -1 O VAL A 365 N VAL A 362 SHEET 1 AA2 2 PHE A 325 GLU A 331 0 SHEET 2 AA2 2 GLU A 334 ILE A 341 -1 O GLU A 334 N GLU A 331 SITE 1 AC1 9 ARG A 312 ARG A 313 ASN A 326 ILE A 327 SITE 2 AC1 9 HIS A 372 HOH A 616 HOH A 640 HOH A 644 SITE 3 AC1 9 HOH A 665 SITE 1 AC2 7 GLU A 310 PRO A 311 LEU A 323 PHE A 325 SITE 2 AC2 7 HOH A 626 HOH A 637 HOH A 640 CRYST1 42.854 42.854 46.909 90.00 90.00 90.00 P 43 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 0.023335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021318 0.00000