HEADER SIGNALING PROTEIN 24-JAN-19 6QJJ TITLE CRYSTAL STRUCTURE OF THE THIRD PDZ DOMAIN OF PSD-95 PROTEIN: SPACE TITLE 2 GROUP P3221 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 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 4 24-JAN-24 6QJJ 1 REMARK REVDAT 3 15-JAN-20 6QJJ 1 REMARK REVDAT 2 24-APR-19 6QJJ 1 JRNL REVDAT 1 17-APR-19 6QJJ 0 SPRSDE 17-APR-19 6QJJ 5OIG 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 16133 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 830 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 18.9465 - 3.0855 1.00 2537 164 0.1817 0.1945 REMARK 3 2 3.0855 - 2.4507 1.00 2542 161 0.2302 0.2396 REMARK 3 3 2.4507 - 2.1414 1.00 2570 132 0.2127 0.2556 REMARK 3 4 2.1414 - 1.9459 0.99 2564 135 0.2092 0.2896 REMARK 3 5 1.9459 - 1.8065 0.99 2543 108 0.2379 0.3148 REMARK 3 6 1.8065 - 1.7001 1.00 2547 130 0.2843 0.4101 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.73 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 6QJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-15 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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 18.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 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 (%): 31.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 30% PEG 4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 75.78133 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 37.89067 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 37.89067 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 75.78133 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: 490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 ASP A 306 REMARK 465 ILE A 307 REMARK 465 PRO A 308 REMARK 465 SER A 398 REMARK 465 ARG A 399 REMARK 465 PHE A 400 REMARK 465 GLU A 401 REMARK 465 ALA A 402 REMARK 465 LYS A 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 SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OIG RELATED DB: PDB REMARK 900 5OIG CONTAINS THE SAME PROTEIN WITH THOSE SIDE CHAINS WITH POOR REMARK 900 ELECTRON DENSITY TRUNCATED AT THE CB DBREF 6QJJ A 305 403 UNP P78352 DLG4_HUMAN 305 403 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 ASP 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 SO4 A 502 5 HET SO4 A 503 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *20(H2 O) HELIX 1 AA1 GLY A 345 SER A 350 1 6 HELIX 2 AA2 SER A 371 ALA A 382 1 12 SHEET 1 AA1 5 ARG A 312 HIS A 317 0 SHEET 2 AA1 5 THR A 385 TYR A 392 -1 O ILE A 388 N ILE A 314 SHEET 3 AA1 5 ASP A 357 VAL A 362 -1 N GLN A 358 O GLN A 391 SHEET 4 AA1 5 GLU A 334 ILE A 341 -1 N ILE A 336 O ILE A 359 SHEET 5 AA1 5 PHE A 325 GLU A 331 -1 N VAL A 328 O PHE A 337 SHEET 1 AA2 4 ARG A 312 HIS A 317 0 SHEET 2 AA2 4 THR A 385 TYR A 392 -1 O ILE A 388 N ILE A 314 SHEET 3 AA2 4 ASP A 357 VAL A 362 -1 N GLN A 358 O GLN A 391 SHEET 4 AA2 4 VAL A 365 ASP A 366 -1 O VAL A 365 N VAL A 362 SITE 1 AC1 5 HIS A 372 GLU A 373 LYS A 393 GLU A 396 SITE 2 AC1 5 HOH A 615 SITE 1 AC2 4 ARG A 313 ARG A 354 LYS A 355 HOH A 601 SITE 1 AC3 5 ARG A 318 THR A 321 GLY A 322 ASP A 332 SITE 2 AC3 5 LYS A 380 CRYST1 34.076 34.076 113.672 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 0.029346 0.016943 0.000000 0.00000 SCALE2 0.000000 0.033886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008797 0.00000