HEADER STRUCTURAL PROTEIN 15-AUG-18 6EEY TITLE CRYSTAL STRUCTURE OF HUMAN SCRIBBLE PDZ4 R1110G MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SCRIBBLE HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ 4 DOMAIN RESIDUES 1098-1189; COMPND 5 SYNONYM: HSCRIB,PROTEIN LAP4; COMPND 6 ENGINEERED: YES; COMPND 7 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: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PDZ DOMAIN, CELL POLARITY, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.M.JANEZIC,P.HSU,C.HAGUE REVDAT 5 11-OCT-23 6EEY 1 REMARK REVDAT 4 01-JAN-20 6EEY 1 REMARK REVDAT 3 16-OCT-19 6EEY 1 JRNL REVDAT 2 09-OCT-19 6EEY 1 JRNL REVDAT 1 02-OCT-19 6EEY 0 JRNL AUTH E.M.JANEZIC,D.A.HARRIS,D.DINH,K.S.LEE,A.STEWART,T.R.HINDS, JRNL AUTH 2 P.L.HSU,N.ZHENG,C.HAGUE JRNL TITL SCRIBBLE CO-OPERATIVELY BINDS MULTIPLE ALPHA1D-ADRENERGIC JRNL TITL 2 RECEPTOR C-TERMINAL PDZ LIGANDS. JRNL REF SCI REP V. 9 14073 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31575922 JRNL DOI 10.1038/S41598-019-50671-6 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.4 REMARK 3 NUMBER OF REFLECTIONS : 20614 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 31.9701 - 2.7582 0.98 1629 175 0.1557 0.1741 REMARK 3 2 2.7582 - 2.1894 1.00 1625 175 0.1561 0.1776 REMARK 3 3 2.1894 - 1.9127 1.00 1621 174 0.1485 0.1723 REMARK 3 4 1.9127 - 1.7378 1.00 1618 173 0.1614 0.1895 REMARK 3 5 1.7378 - 1.6133 1.00 1593 172 0.1574 0.1919 REMARK 3 6 1.6133 - 1.5182 1.00 1602 172 0.1663 0.1971 REMARK 3 7 1.5182 - 1.4421 1.00 1619 174 0.1553 0.1723 REMARK 3 8 1.4421 - 1.3794 1.00 1634 176 0.1621 0.1798 REMARK 3 9 1.3794 - 1.3263 1.00 1602 172 0.1566 0.2063 REMARK 3 10 1.3263 - 1.2805 1.00 1587 170 0.1596 0.1883 REMARK 3 11 1.2805 - 1.2405 0.87 1397 150 0.1660 0.1761 REMARK 3 12 1.2405 - 1.2050 0.51 827 90 0.1603 0.2049 REMARK 3 13 1.2050 - 1.1733 0.15 232 24 0.1435 0.2156 REMARK 3 14 1.1733 - 1.1446 0.02 28 3 0.1536 0.0519 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.10 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 6EEY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236196. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-18 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 : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00004 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 40.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : 0.05400 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 1.13 REMARK 200 STARTING MODEL: 4WYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 0.25 M AMMONIUM NITRATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 20.11750 REMARK 290 SMTRY3 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5850 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 SER A -2 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 126 O HOH A 214 1.91 REMARK 500 O HOH A 147 O HOH A 213 1.93 REMARK 500 O HOH A 142 O HOH A 164 1.94 REMARK 500 NE2 HIS A -1 O HOH A 101 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 103 O HOH A 113 1655 1.88 REMARK 500 O HOH A 132 O HOH A 214 2645 2.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 6EEY A 1098 1189 UNP Q14160 SCRIB_HUMAN 1098 1189 SEQADV 6EEY SER A -2 UNP Q14160 EXPRESSION TAG SEQADV 6EEY HIS A -1 UNP Q14160 EXPRESSION TAG SEQADV 6EEY MET A 0 UNP Q14160 EXPRESSION TAG SEQADV 6EEY GLY A 1110 UNP Q14160 ARG 1110 ENGINEERED MUTATION SEQRES 1 A 95 SER HIS MET LEU ARG GLU LEU CYS ILE GLN LYS ALA PRO SEQRES 2 A 95 GLY GLU GLY LEU GLY ILE SER ILE ARG GLY GLY ALA ARG SEQRES 3 A 95 GLY HIS ALA GLY ASN PRO ARG ASP PRO THR ASP GLU GLY SEQRES 4 A 95 ILE PHE ILE SER LYS VAL SER PRO THR GLY ALA ALA GLY SEQRES 5 A 95 ARG ASP GLY ARG LEU ARG VAL GLY LEU ARG LEU LEU GLU SEQRES 6 A 95 VAL ASN GLN GLN SER LEU LEU GLY LEU THR HIS GLY GLU SEQRES 7 A 95 ALA VAL GLN LEU LEU ARG SER VAL GLY ASP THR LEU THR SEQRES 8 A 95 VAL LEU VAL CYS FORMUL 2 HOH *131(H2 O) HELIX 1 AA1 ASP A 1128 GLU A 1132 5 5 HELIX 2 AA2 GLY A 1143 GLY A 1149 1 7 HELIX 3 AA3 THR A 1169 ARG A 1178 1 10 SHEET 1 AA1 5 ARG A1099 GLN A1104 0 SHEET 2 AA1 5 THR A1183 CYS A1189 -1 O LEU A1184 N ILE A1103 SHEET 3 AA1 5 ARG A1156 VAL A1160 -1 N LEU A1158 O LEU A1187 SHEET 4 AA1 5 ILE A1134 VAL A1139 -1 N ILE A1134 O LEU A1157 SHEET 5 AA1 5 ILE A1113 GLY A1117 -1 N SER A1114 O SER A1137 SHEET 1 AA2 4 ARG A1099 GLN A1104 0 SHEET 2 AA2 4 THR A1183 CYS A1189 -1 O LEU A1184 N ILE A1103 SHEET 3 AA2 4 ARG A1156 VAL A1160 -1 N LEU A1158 O LEU A1187 SHEET 4 AA2 4 GLN A1163 SER A1164 -1 O GLN A1163 N VAL A1160 CRYST1 27.286 40.235 32.260 90.00 97.85 90.00 P 1 21 1 2 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 0.036648 0.000000 0.005053 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031291 0.00000