HEADER SIGNALING PROTEIN 19-MAY-20 6X1N TITLE CRYSTAL STRUCTURE OF CHOANOFLAGELLATE (MONOSIGA BREVICOLLIS) DLG1 PDZ3 TITLE 2 (MBDLG-3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MBDLG-3 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 232-336; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MONOSIGA BREVICOLLIS; SOURCE 3 ORGANISM_COMMON: CHOANOFLAGELLATE; SOURCE 4 ORGANISM_TAXID: 81824; SOURCE 5 GENE: 209; 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: PET28A+ KEYWDS PDZ, PEPTIDE-BINDING DOMAIN, CHOANOFLAGELLATE, SIGNALING, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.MACKLEY,J.F.AMACHER REVDAT 2 18-OCT-23 6X1N 1 REMARK REVDAT 1 25-NOV-20 6X1N 0 JRNL AUTH M.GAO,I.G.P.MACKLEY,S.MESBAHI-VASEY,H.A.BAMONTE, JRNL AUTH 2 S.A.STRUYVENBERG,L.LANDOLT,N.J.PEDERSON,L.I.WILLIAMS, JRNL AUTH 3 C.D.BAHL,L.BROOKS 3RD,J.F.AMACHER JRNL TITL STRUCTURAL CHARACTERIZATION AND COMPUTATIONAL ANALYSIS OF JRNL TITL 2 PDZ DOMAINS IN MONOSIGA BREVICOLLIS. JRNL REF PROTEIN SCI. V. 29 2226 2020 JRNL REFN ESSN 1469-896X JRNL PMID 32914530 JRNL DOI 10.1002/PRO.3947 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 23070 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1126 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 38.5150 - 2.6048 1.00 2822 148 0.1508 0.1576 REMARK 3 2 2.6048 - 2.0676 1.00 2800 151 0.1588 0.1618 REMARK 3 3 2.0676 - 1.8062 1.00 2783 162 0.1570 0.1819 REMARK 3 4 1.8062 - 1.6411 1.00 2798 119 0.1601 0.1643 REMARK 3 5 1.6411 - 1.5234 1.00 2790 122 0.1577 0.1750 REMARK 3 6 1.5234 - 1.4336 1.00 2751 141 0.1619 0.1847 REMARK 3 7 1.4336 - 1.3618 0.99 2734 165 0.1709 0.2007 REMARK 3 8 1.3618 - 1.3030 0.89 2466 118 0.1778 0.1883 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.97 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 : 0.005 830 REMARK 3 ANGLE : 0.839 1120 REMARK 3 CHIRALITY : 0.084 122 REMARK 3 PLANARITY : 0.005 147 REMARK 3 DIHEDRAL : 17.856 308 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 6X1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977410 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23422 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.303 REMARK 200 RESOLUTION RANGE LOW (A) : 38.515 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.160 REMARK 200 R MERGE (I) : 0.02100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.09 REMARK 200 R MERGE FOR SHELL (I) : 0.09600 REMARK 200 R SYM FOR SHELL (I) : 0.13600 REMARK 200 FOR SHELL : 6.250 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 6QJF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M ZINC CHLORIDE, 20% W/V PEG3350, REMARK 280 PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.19200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.37450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.19200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.37450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 DBREF 6X1N A 232 336 UNP A9UT73 A9UT73_MONBE 232 336 SEQRES 1 A 105 LYS MET SER ASP LEU ARG THR VAL THR LEU TYR LYS GLY SEQRES 2 A 105 LYS ALA GLY PHE GLY PHE SER LEU LEU GLY PRO ALA LYS SEQRES 3 A 105 ALA GLY PRO ALA GLU GLU GLY GLU PRO VAL GLY ILE PHE SEQRES 4 A 105 ILE SER ARG ILE LEU PRO GLU GLY ALA ALA ILE GLU SER SEQRES 5 A 105 GLY GLN VAL PHE GLU GLY ASP GLN ILE LEU SER MET ASN SEQRES 6 A 105 GLY GLN ASP LEU ALA LEU ALA SER TYR ARG GLN ALA ALA SEQRES 7 A 105 ASN LEU VAL LYS HIS ILE THR ASP GLY VAL MET THR LEU SEQRES 8 A 105 ASN LEU THR ALA ASN PRO GLY MET TYR ASP LEU TYR LYS SEQRES 9 A 105 GLN HET GOL A 401 6 HET GOL A 402 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *155(H2 O) HELIX 1 AA1 GLY A 278 GLY A 284 1 7 HELIX 2 AA2 SER A 304 HIS A 314 1 11 HELIX 3 AA3 ASN A 327 TYR A 334 1 8 SHEET 1 AA1 5 ARG A 237 TYR A 242 0 SHEET 2 AA1 5 VAL A 319 ALA A 326 -1 O MET A 320 N LEU A 241 SHEET 3 AA1 5 ASP A 290 MET A 295 -1 N GLN A 291 O THR A 325 SHEET 4 AA1 5 ILE A 269 ILE A 274 -1 N ILE A 269 O ILE A 292 SHEET 5 AA1 5 PHE A 250 LEU A 253 -1 N LEU A 253 O PHE A 270 SHEET 1 AA2 4 ARG A 237 TYR A 242 0 SHEET 2 AA2 4 VAL A 319 ALA A 326 -1 O MET A 320 N LEU A 241 SHEET 3 AA2 4 ASP A 290 MET A 295 -1 N GLN A 291 O THR A 325 SHEET 4 AA2 4 GLN A 298 ASP A 299 -1 O GLN A 298 N MET A 295 SITE 1 AC1 10 MET A 233 SER A 234 ASP A 235 ARG A 237 SITE 2 AC1 10 GLN A 285 TYR A 305 HOH A 520 HOH A 524 SITE 3 AC1 10 HOH A 535 HOH A 613 SITE 1 AC2 9 ASP A 235 PHE A 248 PHE A 250 VAL A 312 SITE 2 AC2 9 HOH A 502 HOH A 506 HOH A 575 HOH A 584 SITE 3 AC2 9 HOH A 609 CRYST1 76.384 44.749 28.613 90.00 97.95 90.00 C 1 2 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 0.013092 0.000000 0.001829 0.00000 SCALE2 0.000000 0.022347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035288 0.00000