HEADER TRANSFERASE 22-JUN-09 2WL7 TITLE CRYSTAL STRUCTURE OF THE PSD93 PDZ1 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DISKS LARGE HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ1, RESIDUES 95-188; COMPND 5 SYNONYM: POSTSYNAPTIC DENSITY PROTEIN PSD-93, CHANNEL-ASSOCIATED COMPND 6 PROTEIN OF SYNAPSE-110, CHAPSYN-110, PSD-93; COMPND 7 EC: 2.7.4.8; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS DELTA2 RECEPTOR INTERACTING PROTEIN, TRANSFERASE, DLG2, MAGUK, PSD93, KEYWDS 2 PDZ DOMAIN, CHAPSYN-110 EXPDTA X-RAY DIFFRACTION AUTHOR M.FIORENTINI,A.KALLEHAUGE,O.KRISTENSEN,J.S.KASTRUP,M.GAJHEDE REVDAT 2 13-DEC-23 2WL7 1 REMARK REVDAT 1 19-JAN-10 2WL7 0 JRNL AUTH M.FIORENTINI,A.K.NIELSEN,O.KRISTENSEN,J.S.KASTRUP,M.GAJHEDE JRNL TITL STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN PSD-93. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 65 1254 2009 JRNL REFN ESSN 1744-3091 JRNL PMID 20054121 JRNL DOI 10.1107/S1744309109043267 REMARK 2 REMARK 2 RESOLUTION. 2.03 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 7977 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 800 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 21.7479 - 3.6807 0.99 1194 124 0.1489 0.1881 REMARK 3 2 3.6807 - 2.9237 1.00 1188 144 0.1619 0.1877 REMARK 3 3 2.9237 - 2.5548 1.00 1200 130 0.1745 0.2147 REMARK 3 4 2.5548 - 2.3215 1.00 1182 153 0.1682 0.2116 REMARK 3 5 2.3215 - 2.1553 1.00 1217 111 0.1607 0.2587 REMARK 3 6 2.1553 - 2.0283 0.99 1196 138 0.1677 0.2049 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 : 0.41 REMARK 3 B_SOL : 57.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.870 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.12120 REMARK 3 B22 (A**2) : -2.12120 REMARK 3 B33 (A**2) : 4.24230 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 770 REMARK 3 ANGLE : 0.703 1043 REMARK 3 CHIRALITY : 0.049 115 REMARK 3 PLANARITY : 0.002 139 REMARK 3 DIHEDRAL : 13.946 291 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 2WL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1290040172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7993 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 28.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.200 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: PDB ENTRY 2I1N REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M NICL2, 0.1 M TRIS, PH 8.5, 1 M REMARK 280 LI2SO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.59900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.59454 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.17167 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 42.59900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.59454 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.17167 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 42.59900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.59454 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.17167 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.18909 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 30.34333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 49.18909 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 30.34333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 49.18909 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 30.34333 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -144.5 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2002 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2024 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2063 LIES ON A SPECIAL POSITION. 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 89 REMARK 465 PRO A 90 REMARK 465 LEU A 91 REMARK 465 GLY A 92 REMARK 465 SER A 93 REMARK 465 PRO A 94 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 120 72.58 -161.21 REMARK 500 ASN A 149 -10.59 87.01 REMARK 500 ASN A 156 -114.06 46.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1194 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1193 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST 8 N-TERMINAL RESIDUES ARE CLONING ARTIFACTS REMARK 999 REMAINING FROM THE VECTOR. DBREF 2WL7 A 89 96 PDB 2WL7 2WL7 89 96 DBREF 2WL7 A 97 190 UNP Q91XM9 DLG2_MOUSE 95 188 SEQADV 2WL7 ASP A 125 UNP Q91XM9 GLY 123 CONFLICT SEQRES 1 A 102 GLY PRO LEU GLY SER PRO GLU PHE GLU PHE GLU GLU ILE SEQRES 2 A 102 THR LEU GLU ARG GLY ASN SER GLY LEU GLY PHE SER ILE SEQRES 3 A 102 ALA GLY GLY THR ASP ASN PRO HIS ILE GLY ASP ASP PRO SEQRES 4 A 102 GLY ILE PHE ILE THR LYS ILE ILE PRO GLY GLY ALA ALA SEQRES 5 A 102 ALA GLU ASP GLY ARG LEU ARG VAL ASN ASP CYS ILE LEU SEQRES 6 A 102 ARG VAL ASN GLU VAL ASP VAL SER GLU VAL SER HIS SER SEQRES 7 A 102 LYS ALA VAL GLU ALA LEU LYS GLU ALA GLY SER ILE VAL SEQRES 8 A 102 ARG LEU TYR VAL ARG ARG ARG ARG PRO ILE LEU HET SO4 A1191 5 HET SO4 A1192 5 HET CL A1193 1 HET SO4 A1194 5 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 4 CL CL 1- FORMUL 6 HOH *120(H2 O) HELIX 1 1 GLY A 138 GLY A 144 1 7 HELIX 2 2 SER A 164 ALA A 175 1 12 SHEET 1 AA 5 PHE A 96 GLU A 104 0 SHEET 2 AA 5 ILE A 178 ARG A 186 -1 O VAL A 179 N LEU A 103 SHEET 3 AA 5 CYS A 151 VAL A 155 -1 O CYS A 151 N ARG A 184 SHEET 4 AA 5 ILE A 129 ILE A 134 -1 O ILE A 129 N ILE A 152 SHEET 5 AA 5 PHE A 112 GLY A 116 -1 O SER A 113 N THR A 132 SHEET 1 AB 4 PHE A 96 GLU A 104 0 SHEET 2 AB 4 ILE A 178 ARG A 186 -1 O VAL A 179 N LEU A 103 SHEET 3 AB 4 CYS A 151 VAL A 155 -1 O CYS A 151 N ARG A 184 SHEET 4 AB 4 VAL A 158 ASP A 159 -1 O VAL A 158 N VAL A 155 SITE 1 AC1 4 LYS A 133 ARG A 147 VAL A 148 HOH A2116 SITE 1 AC2 6 ARG A 105 GLY A 106 ASN A 107 SER A 108 SITE 2 AC2 6 HOH A2106 HOH A2120 SITE 1 AC3 5 GLU A 100 THR A 102 ARG A 145 ARG A 154 SITE 2 AC3 5 HOH A2119 SITE 1 AC4 3 THR A 132 ASN A 149 ARG A 186 CRYST1 85.198 85.198 45.515 90.00 90.00 120.00 H 3 9 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 0.011737 0.006777 0.000000 0.00000 SCALE2 0.000000 0.013553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021971 0.00000