HEADER TRANSPORT PROTEIN 03-MAY-11 3RT6 TITLE FLUOROWILLARDIINE BOUND TO THE LIGAND BINDING DOMAIN OF GLUA3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR 3; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: GLUA3, GLUR-3, AMPA-SELECTIVE GLUTAMATE RECEPTOR 3, GLUR-C, COMPND 6 GLUR-K3, GLUTAMATE RECEPTOR IONOTROPIC, AMPA 3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GLUA3, GLUR3, GRIA3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI B(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-22B(+) KEYWDS GLUTAMATE RECEPTOR, GLUR3, AMPA RECEPTOR, S1S2, NEUROTRANSMITTER KEYWDS 2 RECEPTOR, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.H.AHMED,R.E.OSWALD REVDAT 4 13-SEP-23 3RT6 1 REMARK SEQADV LINK REVDAT 3 26-JUL-17 3RT6 1 SOURCE REMARK REVDAT 2 06-JUL-11 3RT6 1 JRNL REVDAT 1 18-MAY-11 3RT6 0 JRNL AUTH K.POON,A.H.AHMED,L.M.NOWAK,R.E.OSWALD JRNL TITL MECHANISMS OF MODAL ACTIVATION OF GLUA3 RECEPTORS. JRNL REF MOL.PHARMACOL. V. 80 49 2011 JRNL REFN ISSN 0026-895X JRNL PMID 21464198 JRNL DOI 10.1124/MOL.111.071688 REMARK 2 REMARK 2 RESOLUTION. 2.84 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) : 2.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 7473 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 750 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 34.3065 - 4.8465 0.98 1477 171 0.2125 0.2521 REMARK 3 2 4.8465 - 3.8485 0.97 1398 149 0.1595 0.2162 REMARK 3 3 3.8485 - 3.3625 0.95 1320 149 0.1786 0.2656 REMARK 3 4 3.3625 - 3.0553 0.94 1309 145 0.2032 0.2639 REMARK 3 5 3.0553 - 2.8364 0.88 1219 136 0.2350 0.3114 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 : 0.36 REMARK 3 B_SOL : 29.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.090 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) : -11.76480 REMARK 3 B22 (A**2) : 8.35980 REMARK 3 B33 (A**2) : 1.31730 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 : 0.008 2096 REMARK 3 ANGLE : 1.084 2822 REMARK 3 CHIRALITY : 0.068 309 REMARK 3 PLANARITY : 0.004 352 REMARK 3 DIHEDRAL : 16.064 785 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 3RT6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065345. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : RH COATED SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7864 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.835 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.17900 REMARK 200 R SYM (I) : 0.17900 REMARK 200 FOR THE DATA SET : 13.3230 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : 0.56800 REMARK 200 FOR SHELL : 4.024 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3DLN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-15% PEG8000, 0.1-0.15 M ZINC REMARK 280 ACETATE, 0.25 M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 68.60800 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 68.60800 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 47.39200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 HIS B 23 -161.83 -59.30 REMARK 500 GLU B 24 -12.62 62.04 REMARK 500 ILE B 85 136.34 -174.39 REMARK 500 LYS B 129 43.92 -99.80 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 FWD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RT8 RELATED DB: PDB REMARK 900 RELATED ID: 3RTF RELATED DB: PDB REMARK 900 RELATED ID: 3RTW RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN IS NATURAL ISOFORM FLIP (P19492-2). PROTEIN FRAGMENT REMARK 999 CONSISTS OF UNP RESIDUES 417-530 AND UNP RESIDUES 658-799 CONNECTED REMARK 999 BY AN ENGINEERED GT LINKER. DBREF 3RT6 B 4 117 UNP P19492 GRIA3_RAT 417 530 DBREF 3RT6 B 120 261 UNP P19492 GRIA3_RAT 658 799 SEQADV 3RT6 GLY B 118 UNP P19492 LINKER SEQADV 3RT6 THR B 119 UNP P19492 LINKER SEQRES 1 B 258 ARG THR ILE VAL VAL THR THR ILE LEU GLU SER PRO TYR SEQRES 2 B 258 VAL MET TYR LYS LYS ASN HIS GLU GLN LEU GLU GLY ASN SEQRES 3 B 258 GLU ARG TYR GLU GLY TYR CYS VAL ASP LEU ALA TYR GLU SEQRES 4 B 258 ILE ALA LYS HIS VAL ARG ILE LYS TYR LYS LEU SER ILE SEQRES 5 B 258 VAL GLY ASP GLY LYS TYR GLY ALA ARG ASP PRO GLU THR SEQRES 6 B 258 LYS ILE TRP ASN GLY MET VAL GLY GLU LEU VAL TYR GLY SEQRES 7 B 258 ARG ALA ASP ILE ALA VAL ALA PRO LEU THR ILE THR LEU SEQRES 8 B 258 VAL ARG GLU GLU VAL ILE ASP PHE SER LYS PRO PHE MET SEQRES 9 B 258 SER LEU GLY ILE SER ILE MET ILE LYS LYS GLY THR PRO SEQRES 10 B 258 ILE GLU SER ALA GLU ASP LEU ALA LYS GLN THR GLU ILE SEQRES 11 B 258 ALA TYR GLY THR LEU ASP SER GLY SER THR LYS GLU PHE SEQRES 12 B 258 PHE ARG ARG SER LYS ILE ALA VAL TYR GLU LYS MET TRP SEQRES 13 B 258 SER TYR MET LYS SER ALA GLU PRO SER VAL PHE THR LYS SEQRES 14 B 258 THR THR ALA ASP GLY VAL ALA ARG VAL ARG LYS SER LYS SEQRES 15 B 258 GLY LYS PHE ALA PHE LEU LEU GLU SER THR MET ASN GLU SEQRES 16 B 258 TYR ILE GLU GLN ARG LYS PRO CYS ASP THR MET LYS VAL SEQRES 17 B 258 GLY GLY ASN LEU ASP SER LYS GLY TYR GLY VAL ALA THR SEQRES 18 B 258 PRO LYS GLY SER ALA LEU GLY THR PRO VAL ASN LEU ALA SEQRES 19 B 258 VAL LEU LYS LEU SER GLU GLN GLY ILE LEU ASP LYS LEU SEQRES 20 B 258 LYS ASN LYS TRP TRP TYR ASP LYS GLY GLU CYS HET FWD B 401 15 HET ZN B 1 1 HETNAM FWD 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN- HETNAM 2 FWD 1-YL)-PROPIONIC ACID HETNAM ZN ZINC ION HETSYN FWD FLUORO-WILLARDIINE FORMUL 2 FWD C7 H8 F N3 O4 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *79(H2 O) HELIX 1 1 GLU B 27 GLU B 30 5 4 HELIX 2 2 GLY B 34 ARG B 48 1 15 HELIX 3 3 ASN B 72 TYR B 80 1 9 HELIX 4 4 THR B 93 GLU B 98 1 6 HELIX 5 5 SER B 123 LYS B 129 1 7 HELIX 6 6 GLY B 141 SER B 150 1 10 HELIX 7 7 ILE B 152 SER B 164 1 13 HELIX 8 8 THR B 173 LYS B 183 1 11 HELIX 9 9 SER B 194 GLU B 201 1 8 HELIX 10 10 LEU B 230 GLN B 244 1 15 HELIX 11 11 GLY B 245 TYR B 256 1 12 SHEET 1 A 3 TYR B 51 ILE B 55 0 SHEET 2 A 3 ILE B 6 THR B 10 1 N VAL B 8 O SER B 54 SHEET 3 A 3 ILE B 85 ALA B 86 1 O ILE B 85 N THR B 9 SHEET 1 B 2 MET B 18 TYR B 19 0 SHEET 2 B 2 TYR B 32 GLU B 33 -1 O GLU B 33 N MET B 18 SHEET 1 C 2 ILE B 100 PHE B 102 0 SHEET 2 C 2 ALA B 223 PRO B 225 -1 O THR B 224 N ASP B 101 SHEET 1 D 2 MET B 107 LEU B 109 0 SHEET 2 D 2 LYS B 218 TYR B 220 -1 O LYS B 218 N LEU B 109 SHEET 1 E 4 ALA B 134 THR B 137 0 SHEET 2 E 4 PHE B 188 GLU B 193 1 O ALA B 189 N ALA B 134 SHEET 3 E 4 ILE B 111 LYS B 116 -1 N MET B 114 O PHE B 190 SHEET 4 E 4 THR B 208 VAL B 211 -1 O VAL B 211 N ILE B 113 SSBOND 1 CYS B 206 CYS B 261 1555 1555 2.20 LINK ZN ZN B 1 NE2 HIS B 23 1555 1555 2.40 CISPEP 1 SER B 14 PRO B 15 0 -0.11 CISPEP 2 GLU B 166 PRO B 167 0 -0.84 CISPEP 3 LYS B 204 PRO B 205 0 10.23 SITE 1 AC1 13 TYR B 61 PRO B 89 LEU B 90 THR B 91 SITE 2 AC1 13 ARG B 96 LEU B 138 GLY B 141 SER B 142 SITE 3 AC1 13 THR B 143 LEU B 192 GLU B 193 MET B 196 SITE 4 AC1 13 HOH B 264 SITE 1 AC2 2 HIS B 23 GLU B 24 CRYST1 48.087 47.392 137.216 90.00 90.00 90.00 P 2 2 21 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 0.020796 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007288 0.00000