HEADER MEMBRANE PROTEIN 17-SEP-98 1GR2 TITLE STRUCTURE OF A GLUTAMATE RECEPTOR LIGAND BINDING CORE (GLUR2) TITLE 2 COMPLEXED WITH KAINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (GLUTAMATE RECEPTOR 2); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: GLUR-B, GLUR-2; COMPND 6 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 ORGAN: BRAIN; 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_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 OTHER_DETAILS: SYNTHETIC GENE KEYWDS EXCITORY NEUROTRANSMITTER RECEPTOR, GLUTAMATE RECEPTOR, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.ARMSTRONG,Y.SUN,G.Q.CHEN,E.GOUAUX REVDAT 4 16-AUG-17 1GR2 1 SOURCE REMARK REVDAT 3 24-FEB-09 1GR2 1 VERSN REVDAT 2 22-DEC-99 1GR2 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 09-DEC-98 1GR2 0 JRNL AUTH N.ARMSTRONG,Y.SUN,G.Q.CHEN,E.GOUAUX JRNL TITL STRUCTURE OF A GLUTAMATE-RECEPTOR LIGAND-BINDING CORE IN JRNL TITL 2 COMPLEX WITH KAINATE. JRNL REF NATURE V. 395 913 1998 JRNL REFN ISSN 0028-0836 JRNL PMID 9804426 JRNL DOI 10.1038/27692 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 19483 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1400 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1869 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.86 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.483 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19209 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.750 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 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 (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM KIPI, PH 5.0, 14% PEG 8K 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 31.53500 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: MONOMERIC 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 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 MET A 4 REMARK 465 GLY A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 ASN A 8 REMARK 465 ASP A 9 REMARK 465 THR A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 LEU A 13 REMARK 465 GLU A 14 REMARK 465 ASN A 15 REMARK 465 ASN A 34 REMARK 465 HIS A 35 REMARK 465 GLU A 36 REMARK 465 LYS A 129 REMARK 465 PRO A 130 REMARK 465 GLY A 131 REMARK 465 THR A 132 REMARK 465 ASP A 133 REMARK 465 GLY A 134 REMARK 465 ASN A 135 REMARK 465 PRO A 136 REMARK 465 ILE A 137 REMARK 465 GLY A 278 REMARK 465 SER A 279 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 LYS A 16 CB CG CD CE NZ REMARK 470 LYS A 33 CB CG CD CE NZ REMARK 470 GLU A 39 CB CG CD OE1 OE2 REMARK 470 LYS A 57 CB CG CD CE NZ REMARK 470 ASP A 79 CB CG OD1 OD2 REMARK 470 LEU A 106 CB CG CD1 CD2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 GLU A 138 CB CG CD OE1 OE2 REMARK 470 SER A 139 CB OG REMARK 470 GLU A 141 CB CG CD OE1 OE2 REMARK 470 LYS A 145 CB CG CD CE NZ REMARK 470 GLN A 146 CB CG CD OE1 NE2 REMARK 470 THR A 147 CB OG1 CG2 REMARK 470 ARG A 165 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 167 CB CG CD CE NZ REMARK 470 GLU A 182 CB CG CD OE1 OE2 REMARK 470 LYS A 199 CB CG CD CE NZ REMARK 470 LYS A 201 CB CG CD CE NZ REMARK 470 SER A 245 CB OG REMARK 470 CYS A 277 O 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 GLU A 25 116.50 -161.51 REMARK 500 THR A 147 -9.65 -145.18 REMARK 500 PRO A 221 21.58 -78.71 REMARK 500 LYS A 234 -159.37 -162.09 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 KAI A 999 DBREF 1GR2 A 6 130 UNP P19491 GRIA2_RAT 404 528 DBREF 1GR2 A 135 279 UNP P19491 GRIA2_RAT 652 796 SEQADV 1GR2 ASN A 135 UNP P19491 SER 652 CONFLICT SEQRES 1 A 279 GLY SER ALA MET GLY SER GLY ASN ASP THR SER GLY LEU SEQRES 2 A 279 GLU ASN LYS THR VAL VAL VAL THR THR ILE LEU GLU SER SEQRES 3 A 279 PRO TYR VAL MET MET LYS LYS ASN HIS GLU MET LEU GLU SEQRES 4 A 279 GLY ASN GLU ARG TYR GLU GLY TYR CYS VAL ASP LEU ALA SEQRES 5 A 279 ALA GLU ILE ALA LYS HIS CYS GLY PHE LYS TYR LYS LEU SEQRES 6 A 279 THR ILE VAL GLY ASP GLY LYS TYR GLY ALA ARG ASP ALA SEQRES 7 A 279 ASP THR LYS ILE TRP ASN GLY MET VAL GLY GLU LEU VAL SEQRES 8 A 279 TYR GLY LYS ALA ASP ILE ALA ILE ALA PRO LEU THR ILE SEQRES 9 A 279 THR LEU VAL ARG GLU GLU VAL ILE ASP PHE SER LYS PRO SEQRES 10 A 279 PHE MET SER LEU GLY ILE SER ILE MET ILE LYS LYS PRO SEQRES 11 A 279 GLY THR ASP GLY ASN PRO ILE GLU SER ALA GLU ASP LEU SEQRES 12 A 279 SER LYS GLN THR GLU ILE ALA TYR GLY THR LEU ASP SER SEQRES 13 A 279 GLY SER THR LYS GLU PHE PHE ARG ARG SER LYS ILE ALA SEQRES 14 A 279 VAL PHE ASP LYS MET TRP THR TYR MET ARG SER ALA GLU SEQRES 15 A 279 PRO SER VAL PHE VAL ARG THR THR ALA GLU GLY VAL ALA SEQRES 16 A 279 ARG VAL ARG LYS SER LYS GLY LYS TYR ALA TYR LEU LEU SEQRES 17 A 279 GLU SER THR MET ASN GLU TYR ILE GLU GLN ARG LYS PRO SEQRES 18 A 279 CYS ASP THR MET LYS VAL GLY GLY ASN LEU ASP SER LYS SEQRES 19 A 279 GLY TYR GLY ILE ALA THR PRO LYS GLY SER SER LEU GLY SEQRES 20 A 279 ASN ALA VAL ASN LEU ALA VAL LEU LYS LEU ASN GLU GLN SEQRES 21 A 279 GLY LEU LEU ASP LYS LEU LYS ASN LYS TRP TRP TYR ASP SEQRES 22 A 279 LYS GLY GLU CYS GLY SER HET KAI A 999 15 HETNAM KAI 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE HETSYN KAI KAINATE FORMUL 2 KAI C10 H15 N O4 FORMUL 3 HOH *175(H2 O) HELIX 1 1 GLY A 40 ARG A 43 5 4 HELIX 2 2 TYR A 47 CYS A 59 1 13 HELIX 3 3 GLY A 85 VAL A 91 1 7 HELIX 4 4 LEU A 106 GLU A 109 1 4 HELIX 5 5 ALA A 140 SER A 144 1 5 HELIX 6 6 SER A 158 ARG A 165 1 8 HELIX 7 7 ALA A 169 ARG A 179 1 11 HELIX 8 8 THR A 190 LYS A 199 1 10 HELIX 9 9 SER A 210 GLN A 218 1 9 HELIX 10 10 LEU A 246 GLU A 259 1 14 HELIX 11 11 LEU A 262 TRP A 271 1 10 SHEET 1 A 2 THR A 17 THR A 22 0 SHEET 2 A 2 LYS A 62 ILE A 67 1 N LYS A 62 O VAL A 18 SHEET 1 B 2 ILE A 112 PHE A 114 0 SHEET 2 B 2 ALA A 239 PRO A 241 -1 N THR A 240 O ASP A 113 SHEET 1 C 2 MET A 119 LEU A 121 0 SHEET 2 C 2 LYS A 234 TYR A 236 -1 N TYR A 236 O MET A 119 SHEET 1 D 4 MET A 225 VAL A 227 0 SHEET 2 D 4 ILE A 123 ILE A 127 -1 N ILE A 127 O MET A 225 SHEET 3 D 4 TYR A 204 GLU A 209 -1 N LEU A 208 O SER A 124 SHEET 4 D 4 ALA A 150 GLY A 152 1 N ALA A 150 O ALA A 205 SSBOND 1 CYS A 222 CYS A 277 1555 1555 2.02 CISPEP 1 SER A 26 PRO A 27 0 -0.27 CISPEP 2 GLU A 182 PRO A 183 0 -0.39 CISPEP 3 LYS A 220 PRO A 221 0 -0.02 SITE 1 AC1 12 GLU A 25 TYR A 73 PRO A 101 THR A 103 SITE 2 AC1 12 ARG A 108 GLY A 157 SER A 158 THR A 159 SITE 3 AC1 12 GLU A 209 MET A 212 HOH A1001 HOH A1084 CRYST1 43.220 63.070 46.320 90.00 92.99 90.00 P 1 21 1 2 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 0.023137 0.000000 0.001208 0.00000 SCALE2 0.000000 0.015855 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021618 0.00000