PDB Short entry for 1Q3O HEADER PEPTIDE BINDING PROTEIN 31-JUL-03 1Q3O TITLE CRYSTAL STRUCTURE OF THE SHANK PDZ-LIGAND COMPLEX REVEALS A CLASS I TITLE 2 PDZ INTERACTION AND A NOVEL PDZ-PDZ DIMERIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHANK1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SHANK1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS SHANK, PDZ, GKAP, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.IM,J.H.LEE,S.H.PARK,S.J.PARK,S.-H.RHO,G.B.KANG,E.KIM,S.H.EOM REVDAT 3 13-MAR-24 1Q3O 1 REMARK REVDAT 2 24-FEB-09 1Q3O 1 VERSN REVDAT 1 27-JAN-04 1Q3O 0 JRNL AUTH Y.J.IM,J.H.LEE,S.H.PARK,S.J.PARK,S.-H.RHO,G.B.KANG,E.KIM, JRNL AUTH 2 S.H.EOM JRNL TITL CRYSTAL STRUCTURE OF THE SHANK PDZ-LIGAND COMPLEX REVEALS A JRNL TITL 2 CLASS I PDZ INTERACTION AND A NOVEL PDZ-PDZ DIMERIZATION JRNL REF J.BIOL.CHEM. V. 278 48099 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12954649 JRNL DOI 10.1074/JBC.M306919200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 708448.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 19150 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 934 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3031 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 154 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1623 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.92000 REMARK 3 B22 (A**2) : -2.18000 REMARK 3 B33 (A**2) : -0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.98000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 51.45 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q3O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000019875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-00; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 110; NULL; NULL REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY; REMARK 200 PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B; BL-18B; BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9205; 0.9201; 0.9180 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; NULL; NULL REMARK 200 OPTICS : MIRRORS; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58394 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 27.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000 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) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37700 REMARK 200 R SYM FOR SHELL (I) : 0.37700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20K, NABR, GLYCEROL, SODIUM REMARK 280 ACETATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 25.17000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 582 REMARK 465 SER A 583 REMARK 465 PRO A 688 REMARK 465 ASP A 689 REMARK 465 MET A 690 REMARK 465 LYS B 610 REMARK 465 ALA B 611 REMARK 465 GLN B 612 REMARK 465 THR B 613 REMARK 465 PRO B 614 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 ALA A 611 59.96 -90.08 REMARK 500 GLU B 616 6.32 -150.92 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 BR A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 105 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q3P RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH THE PEPTIDE LIGAND DBREF 1Q3O A 582 690 UNP Q9WV48 SHAN1_RAT 582 690 DBREF 1Q3O B 582 690 UNP Q9WV48 SHAN1_RAT 582 690 SEQRES 1 A 109 GLY SER ASP TYR ILE ILE LYS GLU LYS THR VAL LEU LEU SEQRES 2 A 109 GLN LYS LYS ASP SER GLU GLY PHE GLY PHE VAL LEU ARG SEQRES 3 A 109 GLY ALA LYS ALA GLN THR PRO ILE GLU GLU PHE THR PRO SEQRES 4 A 109 THR PRO ALA PHE PRO ALA LEU GLN TYR LEU GLU SER VAL SEQRES 5 A 109 ASP GLU GLY GLY VAL ALA TRP ARG ALA GLY LEU ARG MET SEQRES 6 A 109 GLY ASP PHE LEU ILE GLU VAL ASN GLY GLN ASN VAL VAL SEQRES 7 A 109 LYS VAL GLY HIS ARG GLN VAL VAL ASN MET ILE ARG GLN SEQRES 8 A 109 GLY GLY ASN THR LEU MET VAL LYS VAL VAL MET VAL THR SEQRES 9 A 109 ARG HIS PRO ASP MET SEQRES 1 B 109 GLY SER ASP TYR ILE ILE LYS GLU LYS THR VAL LEU LEU SEQRES 2 B 109 GLN LYS LYS ASP SER GLU GLY PHE GLY PHE VAL LEU ARG SEQRES 3 B 109 GLY ALA LYS ALA GLN THR PRO ILE GLU GLU PHE THR PRO SEQRES 4 B 109 THR PRO ALA PHE PRO ALA LEU GLN TYR LEU GLU SER VAL SEQRES 5 B 109 ASP GLU GLY GLY VAL ALA TRP ARG ALA GLY LEU ARG MET SEQRES 6 B 109 GLY ASP PHE LEU ILE GLU VAL ASN GLY GLN ASN VAL VAL SEQRES 7 B 109 LYS VAL GLY HIS ARG GLN VAL VAL ASN MET ILE ARG GLN SEQRES 8 B 109 GLY GLY ASN THR LEU MET VAL LYS VAL VAL MET VAL THR SEQRES 9 B 109 ARG HIS PRO ASP MET HET BR A 101 1 HET BR A 102 1 HET BR A 105 1 HET BR B 103 1 HET BR B 104 1 HETNAM BR BROMIDE ION FORMUL 3 BR 5(BR 1-) FORMUL 8 HOH *94(H2 O) HELIX 1 1 GLY A 637 ALA A 642 1 6 HELIX 2 2 GLY A 662 GLY A 673 1 12 HELIX 3 3 GLY B 637 GLY B 643 1 7 HELIX 4 4 GLY B 662 GLY B 673 1 12 SHEET 1 A 8 GLN A 656 ASN A 657 0 SHEET 2 A 8 PHE A 649 VAL A 653 -1 N VAL A 653 O GLN A 656 SHEET 3 A 8 THR A 676 THR A 685 -1 O VAL A 682 N PHE A 649 SHEET 4 A 8 TYR A 585 GLN A 595 -1 N LEU A 594 O LEU A 677 SHEET 5 A 8 SER B 583 GLN B 595 -1 O ILE B 587 N TYR A 585 SHEET 6 A 8 THR B 676 PRO B 688 -1 O VAL B 681 N LYS B 590 SHEET 7 A 8 PHE B 649 VAL B 653 -1 N PHE B 649 O VAL B 682 SHEET 8 A 8 GLN B 656 ASN B 657 -1 O GLN B 656 N VAL B 653 SHEET 1 B 2 PHE A 604 GLY A 608 0 SHEET 2 B 2 GLN A 628 VAL A 633 -1 O SER A 632 N VAL A 605 SHEET 1 C 2 PHE B 604 GLY B 608 0 SHEET 2 C 2 GLN B 628 VAL B 633 -1 O TYR B 629 N ARG B 607 SITE 1 AC1 3 BR A 102 GLN A 665 ASN A 668 SITE 1 AC2 3 HOH A 16 BR A 101 ARG A 664 SITE 1 AC3 1 PRO B 622 SITE 1 AC4 2 GLN B 628 HIS B 663 SITE 1 AC5 2 HOH A 37 LYS A 660 CRYST1 42.000 50.340 51.770 90.00 106.30 90.00 P 1 21 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 0.023810 0.000000 0.006962 0.00000 SCALE2 0.000000 0.019865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020125 0.00000