HEADER STRUCTURAL PROTEIN 24-JUL-14 4UU6 TITLE CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF PALS1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAGUK P55 SUBFAMILY MEMBER 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN, RESIDUES 251-335; COMPND 5 SYNONYM: PALS1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-2 KEYWDS STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.E.IVANOVA,A.G.PURKISS,N.Q.MCDONALD REVDAT 5 08-MAY-24 4UU6 1 REMARK REVDAT 4 28-FEB-18 4UU6 1 JRNL REVDAT 3 25-MAR-15 4UU6 1 JRNL REVDAT 2 11-MAR-15 4UU6 1 JRNL REVDAT 1 14-JAN-15 4UU6 0 JRNL AUTH M.E.IVANOVA,G.C.FLETCHER,N.O'REILLY,A.G.PURKISS, JRNL AUTH 2 B.J.THOMPSON,N.Q.MCDONALD JRNL TITL STRUCTURES OF THE HUMAN PALS1 PDZ DOMAIN WITH AND WITHOUT JRNL TITL 2 LIGAND SUGGEST GATED ACCESS OF CRB TO THE PDZ JRNL TITL 3 PEPTIDE-BINDING GROOVE. JRNL REF ACTA CRYSTALLOGR. D BIOL. V. 71 555 2015 JRNL REF 2 CRYSTALLOGR. JRNL REFN ESSN 1399-0047 JRNL PMID 25760605 JRNL DOI 10.1107/S139900471402776X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 8721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 412 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 39.6012 - 2.5960 1.00 2894 127 0.1784 0.1881 REMARK 3 2 2.5960 - 2.0605 1.00 2746 139 0.2393 0.2800 REMARK 3 3 2.0605 - 1.8001 1.00 2669 146 0.2505 0.3312 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 : 1.26 REMARK 3 B_SOL : 1.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.17 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 : 0.005 646 REMARK 3 ANGLE : 0.872 869 REMARK 3 CHIRALITY : 0.031 106 REMARK 3 PLANARITY : 0.003 113 REMARK 3 DIHEDRAL : 11.432 240 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 251 THROUGH 335 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5045 -3.1564 -6.3629 REMARK 3 T TENSOR REMARK 3 T11: 0.3855 T22: 0.3928 REMARK 3 T33: 0.1156 T12: 0.0026 REMARK 3 T13: 0.0193 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.1197 L22: 1.8557 REMARK 3 L33: 6.3729 L12: 0.1417 REMARK 3 L13: -0.4660 L23: 0.2883 REMARK 3 S TENSOR REMARK 3 S11: -0.0546 S12: 0.0260 S13: -0.0312 REMARK 3 S21: 0.0016 S22: 0.1016 S23: -0.0137 REMARK 3 S31: 0.0162 S32: -0.0390 S33: -0.0502 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 4UU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1290061251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-13 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8722 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: NULL REMARK 200 REMARK 200 REMARK: MOLECULAR REPLACEMENT SEARCH MODEL BASED ON THE PREVIOUSLY REMARK 200 SOLVED STRUCTURE ALSO TO BE SUBMITTED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085M TRIS (PH 8), 0.17M NA ACETATE, REMARK 280 19% (V/V) GLYCEROL, 25.9% (W/V) PEG 4000, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 44.77500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.07000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.16250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.07000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.07000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.38750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.07000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.07000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.16250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.07000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.07000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.38750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.77500 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 246 REMARK 465 PRO A 247 REMARK 465 LEU A 248 REMARK 465 GLY A 249 REMARK 465 SER A 250 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 THR A 253 OG1 CG2 REMARK 470 GLU A 274 CD OE1 OE2 REMARK 470 MET A 275 CG SD CE REMARK 470 LYS A 285 CE NZ REMARK 470 GLU A 297 CD OE1 OE2 REMARK 470 SER A 335 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 MET A 275 -122.49 54.01 REMARK 500 SER A 281 -65.12 -99.16 REMARK 500 REMARK 500 REMARK: NULL 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 1336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1338 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UU5 RELATED DB: PDB REMARK 900 PDZ-PEPTIDE COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 251-335 DBREF 4UU6 A 251 335 UNP Q8N3R9 MPP5_HUMAN 251 335 SEQADV 4UU6 GLY A 246 UNP Q8N3R9 EXPRESSION TAG SEQADV 4UU6 PRO A 247 UNP Q8N3R9 EXPRESSION TAG SEQADV 4UU6 LEU A 248 UNP Q8N3R9 EXPRESSION TAG SEQADV 4UU6 GLY A 249 UNP Q8N3R9 EXPRESSION TAG SEQADV 4UU6 SER A 250 UNP Q8N3R9 EXPRESSION TAG SEQRES 1 A 90 GLY PRO LEU GLY SER GLY GLU THR VAL LYS ILE VAL ARG SEQRES 2 A 90 ILE GLU LYS ALA ARG ASP ILE PRO LEU GLY ALA THR VAL SEQRES 3 A 90 ARG ASN GLU MET ASP SER VAL ILE ILE SER ARG ILE VAL SEQRES 4 A 90 LYS GLY GLY ALA ALA GLU LYS SER GLY LEU LEU HIS GLU SEQRES 5 A 90 GLY ASP GLU VAL LEU GLU ILE ASN GLY ILE GLU ILE ARG SEQRES 6 A 90 GLY LYS ASP VAL ASN GLU VAL PHE ASP LEU LEU SER ASP SEQRES 7 A 90 MET HIS GLY THR LEU THR PHE VAL LEU ILE PRO SER HET GOL A1336 6 HET CL A1337 1 HET ACT A1338 4 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 CL CL 1- FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 HOH *32(H2 O) HELIX 1 1 GLY A 287 GLY A 293 1 7 HELIX 2 2 ASP A 313 ASP A 323 1 11 SHEET 1 AA 4 LYS A 255 LYS A 261 0 SHEET 2 AA 4 GLY A 326 ILE A 333 -1 O GLY A 326 N LYS A 261 SHEET 3 AA 4 GLU A 300 ILE A 304 -1 O GLU A 300 N ILE A 333 SHEET 4 AA 4 ILE A 307 GLU A 308 -1 O ILE A 307 N ILE A 304 SHEET 1 AB 2 ALA A 269 GLU A 274 0 SHEET 2 AB 2 SER A 277 ILE A 283 -1 O SER A 277 N GLU A 274 SITE 1 AC1 5 PRO A 266 LEU A 267 GLY A 268 ALA A 269 SITE 2 AC1 5 LEU A 321 SITE 1 AC2 2 LYS A 255 ARG A 263 SITE 1 AC3 1 ARG A 282 CRYST1 44.140 44.140 89.550 90.00 90.00 90.00 P 43 21 2 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 0.022655 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011167 0.00000