HEADER PEPTIDE BINDING PROTEIN 01-NOV-18 6MYF TITLE CRYSTAL STRUCTURE OF FREE HUMAN SCRIBBLE PDZ1 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SCRIBBLE HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSCRIB,PROTEIN LAP4; COMPND 5 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: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CELL ADHESION, TIGHT JUNCTION, PDZ BINDING MOTIF BINDING, PEPTIDE KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.SUN,T.HOU,L.GAKHAR,E.J.FUENTES REVDAT 5 11-OCT-23 6MYF 1 REMARK REVDAT 4 23-OCT-19 6MYF 1 JRNL REVDAT 3 21-AUG-19 6MYF 1 JRNL REVDAT 2 17-JUL-19 6MYF 1 JRNL REVDAT 1 10-APR-19 6MYF 0 JRNL AUTH S.AWADIA,F.HUQ,T.R.ARNOLD,S.M.GOICOECHEA,Y.J.SUN,T.HOU, JRNL AUTH 2 G.KREIDER-LETTERMAN,P.MASSIMI,L.BANKS,E.J.FUENTES, JRNL AUTH 3 A.L.MILLER,R.GARCIA-MATA JRNL TITL SGEF FORMS A COMPLEX WITH SCRIBBLE AND DLG1 AND REGULATES JRNL TITL 2 EPITHELIAL JUNCTIONS AND CONTRACTILITY. JRNL REF J.CELL BIOL. V. 218 2699 2019 JRNL REFN ESSN 1540-8140 JRNL PMID 31248911 JRNL DOI 10.1083/JCB.201811114 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 10209 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 542 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 45.6355 - 2.5397 1.00 2588 136 0.1581 0.2147 REMARK 3 2 2.5397 - 2.0159 1.00 2441 162 0.1717 0.1717 REMARK 3 3 2.0159 - 1.7610 1.00 2463 124 0.1752 0.2327 REMARK 3 4 1.7610 - 1.6000 0.90 2175 120 0.2291 0.2955 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 707 REMARK 3 ANGLE : 0.994 957 REMARK 3 CHIRALITY : 0.064 106 REMARK 3 PLANARITY : 0.006 130 REMARK 3 DIHEDRAL : 10.833 417 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.0939 7.2170 -10.7494 REMARK 3 T TENSOR REMARK 3 T11: 0.0906 T22: 0.0873 REMARK 3 T33: 0.0845 T12: -0.0098 REMARK 3 T13: -0.0121 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.9204 L22: 0.6967 REMARK 3 L33: 1.0512 L12: -0.4484 REMARK 3 L13: -0.0425 L23: 0.0564 REMARK 3 S TENSOR REMARK 3 S11: -0.0271 S12: 0.0650 S13: 0.0000 REMARK 3 S21: 0.0237 S22: -0.0073 S23: -0.0265 REMARK 3 S31: -0.0901 S32: 0.0956 S33: 0.0212 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 6MYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000232382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10237 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 45.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.54700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: 2W4F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID PH 3.5, 25% (W/V) PEG REMARK 280 3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 45.61700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.61700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 19.55400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.41200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.55400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.41200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.61700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.55400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.41200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.61700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.55400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 21.41200 REMARK 290 SMTRY3 8 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 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 721 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 723 CG SD CE REMARK 470 LYS A 752 CE NZ REMARK 470 ARG A 762 CG CD NE CZ NH1 NH2 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 HE ARG A 815 O HOH A 903 1.56 REMARK 500 HG1 THR A 730 OE1 GLN A 808 1.56 REMARK 500 HH11 ARG A 810 O HOH A 904 1.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 6MYF A 725 815 UNP Q14160 SCRIB_HUMAN 725 815 SEQADV 6MYF GLY A 721 UNP Q14160 EXPRESSION TAG SEQADV 6MYF ALA A 722 UNP Q14160 EXPRESSION TAG SEQADV 6MYF MET A 723 UNP Q14160 EXPRESSION TAG SEQADV 6MYF GLY A 724 UNP Q14160 EXPRESSION TAG SEQRES 1 A 95 GLY ALA MET GLY GLU GLU LEU THR LEU THR ILE LEU ARG SEQRES 2 A 95 GLN THR GLY GLY LEU GLY ILE SER ILE ALA GLY GLY LYS SEQRES 3 A 95 GLY SER THR PRO TYR LYS GLY ASP ASP GLU GLY ILE PHE SEQRES 4 A 95 ILE SER ARG VAL SER GLU GLU GLY PRO ALA ALA ARG ALA SEQRES 5 A 95 GLY VAL ARG VAL GLY ASP LYS LEU LEU GLU VAL ASN GLY SEQRES 6 A 95 VAL ALA LEU GLN GLY ALA GLU HIS HIS GLU ALA VAL GLU SEQRES 7 A 95 ALA LEU ARG GLY ALA GLY THR ALA VAL GLN MET ARG VAL SEQRES 8 A 95 TRP ARG GLU ARG FORMUL 2 HOH *99(H2 O) HELIX 1 AA1 GLY A 767 GLY A 773 1 7 HELIX 2 AA2 GLU A 792 GLY A 802 1 11 SHEET 1 AA1 5 GLY A 724 LEU A 732 0 SHEET 2 AA1 5 ALA A 806 GLU A 814 -1 O ARG A 813 N GLU A 725 SHEET 3 AA1 5 LYS A 779 VAL A 783 -1 N LEU A 781 O ARG A 810 SHEET 4 AA1 5 ILE A 758 VAL A 763 -1 N ILE A 758 O LEU A 780 SHEET 5 AA1 5 ILE A 740 GLY A 744 -1 N ALA A 743 O PHE A 759 SHEET 1 AA2 4 GLY A 724 LEU A 732 0 SHEET 2 AA2 4 ALA A 806 GLU A 814 -1 O ARG A 813 N GLU A 725 SHEET 3 AA2 4 LYS A 779 VAL A 783 -1 N LEU A 781 O ARG A 810 SHEET 4 AA2 4 VAL A 786 ALA A 787 -1 O VAL A 786 N VAL A 783 CRYST1 39.108 42.824 91.234 90.00 90.00 90.00 C 2 2 21 8 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 0.025570 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023351 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010961 0.00000