HEADER SIGNALING PROTEIN 24-JAN-19 6QJL TITLE CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN OF PSD-95 PROTEIN D332G TITLE 2 MUTANT: SPACE GROUP P21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 4; COMPND 3 CHAIN: A, B; 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 6QJL 1 REMARK REVDAT 2 24-APR-19 6QJL 1 JRNL REVDAT 1 17-APR-19 6QJL 0 SPRSDE 17-APR-19 6QJL 5OII 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. 1.04 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 153886 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 7713 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 31.8362 - 3.2391 0.98 4829 257 0.1569 0.1781 REMARK 3 2 3.2391 - 2.5713 0.99 4733 326 0.1551 0.1677 REMARK 3 3 2.5713 - 2.2464 0.98 4860 248 0.1444 0.1716 REMARK 3 4 2.2464 - 2.0411 0.98 4766 279 0.1291 0.1615 REMARK 3 5 2.0411 - 1.8948 0.98 4855 218 0.1370 0.1661 REMARK 3 6 1.8948 - 1.7831 0.98 4789 265 0.1369 0.1653 REMARK 3 7 1.7831 - 1.6938 0.99 4810 322 0.1363 0.1703 REMARK 3 8 1.6938 - 1.6201 0.99 4756 329 0.1361 0.1408 REMARK 3 9 1.6201 - 1.5577 0.99 4840 271 0.1364 0.1824 REMARK 3 10 1.5577 - 1.5039 0.99 4872 271 0.1356 0.1384 REMARK 3 11 1.5039 - 1.4569 1.00 4886 234 0.1349 0.1627 REMARK 3 12 1.4569 - 1.4153 1.00 4962 215 0.1404 0.1578 REMARK 3 13 1.4153 - 1.3780 1.00 4955 177 0.1459 0.1495 REMARK 3 14 1.3780 - 1.3444 1.00 4923 258 0.1442 0.1898 REMARK 3 15 1.3444 - 1.3138 1.00 4926 232 0.1467 0.1520 REMARK 3 16 1.3138 - 1.2859 1.00 4930 243 0.1528 0.1770 REMARK 3 17 1.2859 - 1.2601 1.00 4873 281 0.1503 0.1829 REMARK 3 18 1.2601 - 1.2364 1.00 4852 273 0.1553 0.1934 REMARK 3 19 1.2364 - 1.2143 1.00 4852 289 0.1636 0.2048 REMARK 3 20 1.2143 - 1.1937 1.00 4978 217 0.1658 0.2295 REMARK 3 21 1.1937 - 1.1744 1.00 4831 248 0.1644 0.1620 REMARK 3 22 1.1744 - 1.1564 1.00 4957 264 0.1738 0.1916 REMARK 3 23 1.1564 - 1.1394 0.99 4866 223 0.1774 0.1842 REMARK 3 24 1.1394 - 1.1233 1.00 4982 214 0.1860 0.2052 REMARK 3 25 1.1233 - 1.1081 1.00 4900 248 0.1972 0.2299 REMARK 3 26 1.1081 - 1.0937 1.00 4936 245 0.1999 0.2459 REMARK 3 27 1.0937 - 1.0801 1.00 4813 269 0.2108 0.2409 REMARK 3 28 1.0801 - 1.0671 1.00 4888 257 0.2232 0.2667 REMARK 3 29 1.0671 - 1.0547 1.00 4906 288 0.2290 0.2477 REMARK 3 30 1.0547 - 1.0428 1.00 4847 252 0.2419 0.2498 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.50 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 6QJL 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_1292100289. 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 : 153886 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 47.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.47500 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: 5OIH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 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 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 23.51150 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: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 300 REMARK 465 GLY A 301 REMARK 465 LEU A 302 REMARK 465 GLY A 303 REMARK 465 ALA A 402 REMARK 465 LYS A 403 REMARK 465 MET B 300 REMARK 465 GLY B 301 REMARK 465 LEU B 302 REMARK 465 GLY B 303 REMARK 465 GLU B 304 REMARK 465 GLU B 305 REMARK 465 ALA B 402 REMARK 465 LYS B 403 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 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OII RELATED DB: PDB REMARK 900 5OII CONTAINS THE SAME PROTEIN WITH THOSE SIDE CHAINS WITH POOR REMARK 900 ELEECTRON DENSITY TRUNCATED AT THE CB DBREF 6QJL A 302 403 UNP P78352 DLG4_HUMAN 302 403 DBREF 6QJL B 302 403 UNP P78352 DLG4_HUMAN 302 403 SEQADV 6QJL MET A 300 UNP P78352 INITIATING METHIONINE SEQADV 6QJL GLY A 301 UNP P78352 EXPRESSION TAG SEQADV 6QJL GLY A 332 UNP P78352 ASP 332 ENGINEERED MUTATION SEQADV 6QJL MET B 300 UNP P78352 INITIATING METHIONINE SEQADV 6QJL GLY B 301 UNP P78352 EXPRESSION TAG SEQADV 6QJL GLY B 332 UNP P78352 ASP 332 ENGINEERED MUTATION SEQRES 1 A 104 MET GLY LEU GLY GLU GLU ASP ILE PRO ARG GLU PRO ARG SEQRES 2 A 104 ARG ILE VAL ILE HIS ARG GLY SER THR GLY LEU GLY PHE SEQRES 3 A 104 ASN ILE VAL GLY GLY GLU GLY GLY GLU GLY ILE PHE ILE SEQRES 4 A 104 SER PHE ILE LEU ALA GLY GLY PRO ALA ASP LEU SER GLY SEQRES 5 A 104 GLU LEU ARG LYS GLY ASP GLN ILE LEU SER VAL ASN GLY SEQRES 6 A 104 VAL ASP LEU ARG ASN ALA SER HIS GLU GLN ALA ALA ILE SEQRES 7 A 104 ALA LEU LYS ASN ALA GLY GLN THR VAL THR ILE ILE ALA SEQRES 8 A 104 GLN TYR LYS PRO GLU GLU TYR SER ARG PHE GLU ALA LYS SEQRES 1 B 104 MET GLY LEU GLY GLU GLU ASP ILE PRO ARG GLU PRO ARG SEQRES 2 B 104 ARG ILE VAL ILE HIS ARG GLY SER THR GLY LEU GLY PHE SEQRES 3 B 104 ASN ILE VAL GLY GLY GLU GLY GLY GLU GLY ILE PHE ILE SEQRES 4 B 104 SER PHE ILE LEU ALA GLY GLY PRO ALA ASP LEU SER GLY SEQRES 5 B 104 GLU LEU ARG LYS GLY ASP GLN ILE LEU SER VAL ASN GLY SEQRES 6 B 104 VAL ASP LEU ARG ASN ALA SER HIS GLU GLN ALA ALA ILE SEQRES 7 B 104 ALA LEU LYS ASN ALA GLY GLN THR VAL THR ILE ILE ALA SEQRES 8 B 104 GLN TYR LYS PRO GLU GLU TYR SER ARG PHE GLU ALA LYS HET SO4 A 501 5 HET GOL A 502 9 HET SO4 B 501 5 HET GOL B 502 9 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *208(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 GLU A 401 1 9 HELIX 4 AA4 GLY B 345 GLY B 351 1 7 HELIX 5 AA5 SER B 371 ASN B 381 1 11 HELIX 6 AA6 LYS B 393 GLU B 401 1 9 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 LEU A 360 O ILE A 389 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 PHE A 337 N VAL A 328 SHEET 1 AA3 4 ARG B 312 HIS B 317 0 SHEET 2 AA3 4 THR B 385 TYR B 392 -1 O ILE B 388 N ILE B 314 SHEET 3 AA3 4 ASP B 357 VAL B 362 -1 N GLN B 358 O GLN B 391 SHEET 4 AA3 4 VAL B 365 ASP B 366 -1 O VAL B 365 N VAL B 362 SHEET 1 AA4 2 PHE B 325 GLU B 331 0 SHEET 2 AA4 2 GLU B 334 ILE B 341 -1 O PHE B 337 N VAL B 328 SITE 1 AC1 5 ARG A 312 ARG A 313 HOH A 604 HOH A 611 SITE 2 AC1 5 HOH A 642 SITE 1 AC2 3 GLU A 310 PRO A 311 HOH A 642 SITE 1 AC3 6 GLY A 319 SER A 320 HOH A 692 GLN B 384 SITE 2 AC3 6 THR B 385 HOH B 642 SITE 1 AC4 3 GLU B 310 PRO B 311 HOH B 644 CRYST1 41.313 47.023 43.253 90.00 92.19 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 0.024205 0.000000 0.000926 0.00000 SCALE2 0.000000 0.021266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023137 0.00000