HEADER PROTEIN BINDING 01-MAR-07 2EGO TITLE CRYSTAL STRUCTURE OF TAMALIN PDZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL RECEPTOR FOR PHOSPHOINOSITIDES 1-ASSOCIATED COMPND 3 SCAFFOLD PROTEIN; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: PDZ DOMAIN; COMPND 6 SYNONYM: GRP1-ASSOCIATED SCAFFOLD PROTEIN, TAMALIN, 95 KDA COMPND 7 POSTSYNAPTIC DENSITY PROTEIN DISCS-LARGE ZO-1 DOMAIN-CONTAINING COMPND 8 PROTEIN, PSD-95 PDZ DOMAIN-CONTAINING PROTEIN; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 TISSUE: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T-1 KEYWDS PDZ DOMAIN, LIGAND-FREE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.SUGI,T.OYAMA,T.MUTO,S.NAKANISHI,K.MORIKAWA,H.JINGAMI REVDAT 5 25-OCT-23 2EGO 1 REMARK REVDAT 4 10-NOV-21 2EGO 1 SEQADV REVDAT 3 24-FEB-09 2EGO 1 VERSN REVDAT 2 04-DEC-07 2EGO 1 REMARK REVDAT 1 01-MAY-07 2EGO 0 JRNL AUTH T.SUGI,T.OYAMA,T.MUTO,S.NAKANISHI,K.MORIKAWA,H.JINGAMI JRNL TITL CRYSTAL STRUCTURES OF AUTOINHIBITORY PDZ DOMAIN OF TAMALIN: JRNL TITL 2 IMPLICATIONS FOR METABOTROPIC GLUTAMATE RECEPTOR TRAFFICKING JRNL TITL 3 REGULATION JRNL REF EMBO J. V. 26 2192 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17396155 JRNL DOI 10.1038/SJ.EMBOJ.7601651 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 233285.590 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 17.7 REMARK 3 NUMBER OF REFLECTIONS : 18300 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) : 0.235 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 319 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.034 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) (%) : 11.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 633 REMARK 3 BIN R VALUE (WORKING SET) : 0.5870 REMARK 3 BIN FREE R VALUE : 0.6040 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 20 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.135 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1369 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : -1.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 34.33000 REMARK 3 B22 (A**2) : -19.42000 REMARK 3 B33 (A**2) : -14.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -15.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : -0.3 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 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) : 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 10.00 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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000026641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 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) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.27600 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1G9O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M POTASSIUM REMARK 280 FLUORIDE, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.64100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.01700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.64100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.01700 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: 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 94 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 ARG A 123 REMARK 465 GLU A 124 REMARK 465 GLU A 125 REMARK 465 GLN A 126 REMARK 465 ARG A 127 REMARK 465 GLY B 94 REMARK 465 ARG B 123 REMARK 465 GLU B 124 REMARK 465 GLU B 125 REMARK 465 GLN B 126 REMARK 465 ARG B 127 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 VAL A 128 CB CG1 CG2 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 ASN A 108 40.64 -90.14 REMARK 500 GLU A 129 -126.06 38.46 REMARK 500 GLU B 163 -88.65 -22.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EGK RELATED DB: PDB REMARK 900 TAMALIN PDZ-INTRINSIC LIGAND FUSION PROTEIN REMARK 900 RELATED ID: 2EGN RELATED DB: PDB REMARK 900 TAMALIN PDZ DOMAIN IN COMPLEX WITH MGLUR5 C-TERMINAL PEPTIDE DBREF 2EGO A 96 189 UNP Q8R4T5 GRASP_RAT 96 189 DBREF 2EGO B 96 189 UNP Q8R4T5 GRASP_RAT 96 189 SEQADV 2EGO GLY A 94 UNP Q8R4T5 EXPRESSION TAG SEQADV 2EGO SER A 95 UNP Q8R4T5 EXPRESSION TAG SEQADV 2EGO ALA A 135 UNP Q8R4T5 CYS 135 ENGINEERED MUTATION SEQADV 2EGO GLY B 94 UNP Q8R4T5 EXPRESSION TAG SEQADV 2EGO SER B 95 UNP Q8R4T5 EXPRESSION TAG SEQADV 2EGO ALA B 135 UNP Q8R4T5 CYS 135 ENGINEERED MUTATION SEQRES 1 A 96 GLY SER GLN GLN ARG LYS VAL LEU THR LEU GLU LYS GLY SEQRES 2 A 96 ASP ASN GLN THR PHE GLY PHE GLU ILE GLN THR TYR GLY SEQRES 3 A 96 LEU HIS HIS ARG GLU GLU GLN ARG VAL GLU MET VAL THR SEQRES 4 A 96 PHE VAL ALA ARG VAL HIS GLU SER SER PRO ALA GLN LEU SEQRES 5 A 96 ALA GLY LEU THR PRO GLY ASP THR ILE ALA SER VAL ASN SEQRES 6 A 96 GLY LEU ASN VAL GLU GLY ILE ARG HIS ARG GLU ILE VAL SEQRES 7 A 96 ASP ILE ILE LYS ALA SER GLY ASN VAL LEU ARG LEU GLU SEQRES 8 A 96 THR LEU TYR GLY THR SEQRES 1 B 96 GLY SER GLN GLN ARG LYS VAL LEU THR LEU GLU LYS GLY SEQRES 2 B 96 ASP ASN GLN THR PHE GLY PHE GLU ILE GLN THR TYR GLY SEQRES 3 B 96 LEU HIS HIS ARG GLU GLU GLN ARG VAL GLU MET VAL THR SEQRES 4 B 96 PHE VAL ALA ARG VAL HIS GLU SER SER PRO ALA GLN LEU SEQRES 5 B 96 ALA GLY LEU THR PRO GLY ASP THR ILE ALA SER VAL ASN SEQRES 6 B 96 GLY LEU ASN VAL GLU GLY ILE ARG HIS ARG GLU ILE VAL SEQRES 7 B 96 ASP ILE ILE LYS ALA SER GLY ASN VAL LEU ARG LEU GLU SEQRES 8 B 96 THR LEU TYR GLY THR FORMUL 3 HOH *107(H2 O) HELIX 1 1 SER A 141 ALA A 146 1 6 HELIX 2 2 ARG A 166 SER A 177 1 12 HELIX 3 3 SER B 141 GLY B 147 1 7 HELIX 4 4 ARG B 166 SER B 177 1 12 SHEET 1 A 4 ARG A 98 GLU A 104 0 SHEET 2 A 4 VAL A 180 LEU A 186 -1 O LEU A 183 N LEU A 101 SHEET 3 A 4 THR A 153 VAL A 157 -1 N ALA A 155 O GLU A 184 SHEET 4 A 4 LEU A 160 ASN A 161 -1 O LEU A 160 N VAL A 157 SHEET 1 B 2 PHE A 113 GLY A 119 0 SHEET 2 B 2 MET A 130 VAL A 137 -1 O VAL A 131 N TYR A 118 SHEET 1 C 4 ARG B 98 GLU B 104 0 SHEET 2 C 4 VAL B 180 LEU B 186 -1 O LEU B 183 N LEU B 101 SHEET 3 C 4 THR B 153 VAL B 157 -1 N ALA B 155 O GLU B 184 SHEET 4 C 4 LEU B 160 ASN B 161 -1 O LEU B 160 N VAL B 157 SHEET 1 D 2 PHE B 113 LEU B 120 0 SHEET 2 D 2 GLU B 129 VAL B 137 -1 O PHE B 133 N GLN B 116 CRYST1 111.282 30.034 80.111 90.00 132.33 90.00 C 1 2 1 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 0.008986 0.000000 0.008185 0.00000 SCALE2 0.000000 0.033296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016884 0.00000