HEADER SIGNALING PROTEIN 19-MAY-20 6X1X TITLE PDZ DOMAIN FROM CHOANOFLAGELLATE GIPC (MBGIPC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MBGIPC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN (UNP RESIDUES 94-187); 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: 39217; 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, PROTEIN-PROTEIN INTERACTION, PEPTIDE-BINDING DOMAIN, KEYWDS 2 CHOANOFLAGELLATE, MONOSIGA BREVICOLLIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.GAO,J.F.AMACHER REVDAT 2 18-OCT-23 6X1X 1 REMARK REVDAT 1 25-NOV-20 6X1X 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 27011 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1335 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 41.3860 - 2.5803 1.00 2850 156 0.1643 0.1849 REMARK 3 2 2.5803 - 2.0481 1.00 2747 125 0.1640 0.1754 REMARK 3 3 2.0481 - 1.7892 1.00 2672 148 0.1648 0.1727 REMARK 3 4 1.7892 - 1.6256 1.00 2669 152 0.1673 0.2002 REMARK 3 5 1.6256 - 1.5091 1.00 2665 131 0.1583 0.1964 REMARK 3 6 1.5091 - 1.4201 1.00 2631 150 0.1651 0.1979 REMARK 3 7 1.4201 - 1.3490 1.00 2646 118 0.1688 0.1894 REMARK 3 8 1.3490 - 1.2903 0.99 2621 128 0.1711 0.2013 REMARK 3 9 1.2903 - 1.2406 0.91 2378 136 0.1821 0.2172 REMARK 3 10 1.2406 - 1.1980 0.68 1797 91 0.2064 0.2605 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.37 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 : 0.005 779 REMARK 3 ANGLE : 0.818 1053 REMARK 3 CHIRALITY : 0.086 119 REMARK 3 PLANARITY : 0.005 139 REMARK 3 DIHEDRAL : 15.313 305 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 6X1X 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_1000249422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7 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 : 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 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.198 REMARK 200 RESOLUTION RANGE LOW (A) : 41.386 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 5.340 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.91400 REMARK 200 FOR THE DATA SET : 31.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.63 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11500 REMARK 200 FOR SHELL : 5.150 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 5V6B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM TARTRATE DIBASIC, PH REMARK 280 7.0, 12% W/V PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.85450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.38650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.65050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.38650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.85450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.65050 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: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6180 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 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 GLY A 92 REMARK 465 PRO A 93 REMARK 465 LYS A 94 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 329 O HOH A 355 2.17 REMARK 500 O HOH A 310 O HOH A 451 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 489 DISTANCE = 6.28 ANGSTROMS 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 201 DBREF 6X1X A 94 187 UNP A9VCZ3 A9VCZ3_MONBE 94 187 SEQADV 6X1X GLY A 92 UNP A9VCZ3 EXPRESSION TAG SEQADV 6X1X PRO A 93 UNP A9VCZ3 EXPRESSION TAG SEQRES 1 A 96 GLY PRO LYS GLY THR GLU LYS THR VAL LYS VAL ILE LYS SEQRES 2 A 96 ASP GLY PRO ALA LEU GLY LEU THR ILE SER ASP ASN GLY SEQRES 3 A 96 ALA GLY TYR ALA PHE ILE LYS LYS ILE ARG GLU ASP SER SEQRES 4 A 96 ILE MET SER ARG VAL ALA ASN VAL ALA VAL GLY ASP HIS SEQRES 5 A 96 ILE ALA LYS ILE ASN GLY THR ASP LEU ASN GLY CYS ARG SEQRES 6 A 96 HIS PHE GLU VAL ALA ARG MET LEU LYS GLU ILE PRO ILE SEQRES 7 A 96 GLY SER GLU PHE THR MET ILE CYS VAL GLU PRO LYS LYS SEQRES 8 A 96 SER PHE ASP GLU ILE HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *189(H2 O) HELIX 1 AA1 ARG A 156 ILE A 167 1 12 SHEET 1 AA1 4 GLU A 97 ILE A 103 0 SHEET 2 AA1 4 GLU A 172 VAL A 178 -1 O CYS A 177 N LYS A 98 SHEET 3 AA1 4 HIS A 143 ILE A 147 -1 N HIS A 143 O VAL A 178 SHEET 4 AA1 4 THR A 150 ASP A 151 -1 O THR A 150 N ILE A 147 SHEET 1 AA2 2 LEU A 111 SER A 114 0 SHEET 2 AA2 2 PHE A 122 ILE A 126 -1 O LYS A 124 N THR A 112 SITE 1 AC1 10 VAL A 102 ILE A 103 HIS A 157 SER A 183 SITE 2 AC1 10 HOH A 304 HOH A 308 HOH A 313 HOH A 315 SITE 3 AC1 10 HOH A 357 HOH A 376 CRYST1 29.709 35.301 82.773 90.00 90.00 90.00 P 21 21 21 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 0.033660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012081 0.00000