HEADER MEMBRANE PROTEIN 24-APR-13 4KCD TITLE CRYSTAL STRUCTURE OF THE NMDA RECEPTOR GLUN3A LIGAND BINDING DOMAIN TITLE 2 APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RECEPTOR IONOTROPIC, NMDA 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (UNP RESIDUES 511-660, 776-915); COMPND 5 SYNONYM: GLUN3A, GLUTAMATE RECEPTOR CHI-1, N-METHYL-D-ASPARTATE COMPND 6 RECEPTOR, N-METHYL-D-ASPARTATE RECEPTOR SUBTYPE 3A, NMDAR3A, NR3A, COMPND 7 NMDAR-L, NMDAR-L1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GRIN3A; 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: PET22 MODIFIED KEYWDS MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAO,A.Y.LAU,M.L.MAYER REVDAT 4 20-SEP-23 4KCD 1 REMARK SEQADV REVDAT 3 02-AUG-17 4KCD 1 SOURCE REMARK REVDAT 2 06-NOV-13 4KCD 1 JRNL REVDAT 1 31-JUL-13 4KCD 0 JRNL AUTH Y.YAO,J.BELCHER,A.J.BERGER,M.L.MAYER,A.Y.LAU JRNL TITL CONFORMATIONAL ANALYSIS OF NMDA RECEPTOR GLUN1, GLUN2, AND JRNL TITL 2 GLUN3 LIGAND-BINDING DOMAINS REVEALS SUBTYPE-SPECIFIC JRNL TITL 3 CHARACTERISTICS. JRNL REF STRUCTURE V. 21 1788 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23972471 JRNL DOI 10.1016/J.STR.2013.07.011 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 71098 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3567 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 29.4537 - 4.9051 1.00 2943 151 0.2000 0.2063 REMARK 3 2 4.9051 - 3.8962 1.00 2818 142 0.1350 0.1639 REMARK 3 3 3.8962 - 3.4045 1.00 2769 147 0.1540 0.1658 REMARK 3 4 3.4045 - 3.0936 1.00 2761 153 0.1603 0.1796 REMARK 3 5 3.0936 - 2.8721 1.00 2756 146 0.1559 0.1717 REMARK 3 6 2.8721 - 2.7029 1.00 2718 148 0.1562 0.1892 REMARK 3 7 2.7029 - 2.5676 1.00 2746 134 0.1567 0.2110 REMARK 3 8 2.5676 - 2.4559 0.99 2687 142 0.1545 0.1903 REMARK 3 9 2.4559 - 2.3614 0.99 2722 137 0.1510 0.1916 REMARK 3 10 2.3614 - 2.2799 0.99 2721 145 0.1459 0.1863 REMARK 3 11 2.2799 - 2.2087 0.99 2668 145 0.1400 0.1853 REMARK 3 12 2.2087 - 2.1455 0.99 2710 130 0.1343 0.1453 REMARK 3 13 2.1455 - 2.0891 0.99 2685 149 0.1369 0.1482 REMARK 3 14 2.0891 - 2.0381 0.99 2687 139 0.1398 0.1715 REMARK 3 15 2.0381 - 1.9918 0.99 2677 155 0.1400 0.1893 REMARK 3 16 1.9918 - 1.9494 0.99 2647 146 0.1424 0.2064 REMARK 3 17 1.9494 - 1.9104 0.98 2647 139 0.1442 0.1750 REMARK 3 18 1.9104 - 1.8744 0.98 2659 137 0.1513 0.1885 REMARK 3 19 1.8744 - 1.8409 0.98 2677 138 0.1447 0.1879 REMARK 3 20 1.8409 - 1.8097 0.98 2658 136 0.1503 0.1659 REMARK 3 21 1.8097 - 1.7805 0.98 2637 134 0.1588 0.2215 REMARK 3 22 1.7805 - 1.7531 0.98 2644 153 0.1648 0.2272 REMARK 3 23 1.7531 - 1.7274 0.98 2650 139 0.1649 0.1916 REMARK 3 24 1.7274 - 1.7030 0.98 2605 141 0.1712 0.2446 REMARK 3 25 1.7030 - 1.6800 0.98 2639 141 0.1852 0.2640 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 : 0.40 REMARK 3 B_SOL : 40.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07640 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -0.36360 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 : 0.010 4899 REMARK 3 ANGLE : 1.307 6675 REMARK 3 CHIRALITY : 0.080 725 REMARK 3 PLANARITY : 0.007 874 REMARK 3 DIHEDRAL : 12.215 1828 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 4:143) REMARK 3 ORIGIN FOR THE GROUP (A): -4.3774 -2.8409 -25.0859 REMARK 3 T TENSOR REMARK 3 T11: 0.0493 T22: 0.0572 REMARK 3 T33: 0.0526 T12: -0.0120 REMARK 3 T13: -0.0204 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.0417 L22: 1.3388 REMARK 3 L33: 2.1931 L12: 0.2472 REMARK 3 L13: 0.6696 L23: 0.5829 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: 0.1133 S13: 0.0757 REMARK 3 S21: -0.1016 S22: -0.0399 S23: 0.2087 REMARK 3 S31: -0.0476 S32: -0.1010 S33: 0.0101 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 144:164) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9964 6.0122 -1.2140 REMARK 3 T TENSOR REMARK 3 T11: 0.0766 T22: 0.1624 REMARK 3 T33: 0.1227 T12: -0.0167 REMARK 3 T13: -0.0012 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.8523 L22: 4.4060 REMARK 3 L33: 2.6892 L12: -0.6836 REMARK 3 L13: 0.0146 L23: -0.8745 REMARK 3 S TENSOR REMARK 3 S11: -0.0586 S12: -0.3305 S13: 0.2956 REMARK 3 S21: 0.5569 S22: -0.0231 S23: -0.2827 REMARK 3 S31: -0.1608 S32: 0.3441 S33: 0.0348 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 165:198) REMARK 3 ORIGIN FOR THE GROUP (A): 8.2764 -3.6177 1.4990 REMARK 3 T TENSOR REMARK 3 T11: 0.1028 T22: 0.0958 REMARK 3 T33: 0.0736 T12: 0.0067 REMARK 3 T13: 0.0377 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 1.9021 L22: 2.5059 REMARK 3 L33: 2.0660 L12: -0.6403 REMARK 3 L13: -0.5659 L23: -0.1396 REMARK 3 S TENSOR REMARK 3 S11: -0.1435 S12: -0.2535 S13: -0.1455 REMARK 3 S21: 0.1952 S22: 0.0161 S23: 0.0417 REMARK 3 S31: 0.3790 S32: -0.0278 S33: 0.0723 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 199:292) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9393 3.9424 -17.0040 REMARK 3 T TENSOR REMARK 3 T11: 0.0709 T22: 0.0812 REMARK 3 T33: 0.0845 T12: -0.0316 REMARK 3 T13: 0.0186 T23: 0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.0313 L22: 0.3912 REMARK 3 L33: 1.7292 L12: 0.0246 REMARK 3 L13: 0.6046 L23: -0.0955 REMARK 3 S TENSOR REMARK 3 S11: -0.0257 S12: 0.1396 S13: 0.1101 REMARK 3 S21: -0.0507 S22: 0.0474 S23: -0.0333 REMARK 3 S31: -0.1477 S32: 0.1982 S33: -0.0492 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 4:64) REMARK 3 ORIGIN FOR THE GROUP (A): 44.7774 -3.9175 -7.1515 REMARK 3 T TENSOR REMARK 3 T11: 0.0700 T22: 0.1890 REMARK 3 T33: 0.1210 T12: 0.0119 REMARK 3 T13: 0.0134 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 1.4709 L22: 1.3410 REMARK 3 L33: 1.8769 L12: 0.5018 REMARK 3 L13: 0.2695 L23: 0.3139 REMARK 3 S TENSOR REMARK 3 S11: 0.0350 S12: -0.2825 S13: 0.0679 REMARK 3 S21: 0.0663 S22: -0.0221 S23: -0.1269 REMARK 3 S31: -0.0165 S32: 0.3848 S33: -0.0128 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 65:142) REMARK 3 ORIGIN FOR THE GROUP (A): 37.7737 -15.5500 -12.5293 REMARK 3 T TENSOR REMARK 3 T11: 0.1057 T22: 0.0794 REMARK 3 T33: 0.0997 T12: 0.0541 REMARK 3 T13: 0.0280 T23: 0.0398 REMARK 3 L TENSOR REMARK 3 L11: 1.4598 L22: 1.1572 REMARK 3 L33: 1.4802 L12: 0.2944 REMARK 3 L13: -0.1486 L23: 0.0946 REMARK 3 S TENSOR REMARK 3 S11: -0.0893 S12: -0.2325 S13: -0.1979 REMARK 3 S21: -0.0077 S22: 0.0263 S23: -0.1478 REMARK 3 S31: 0.2620 S32: 0.1342 S33: -0.0105 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN B AND RESID 143:249) REMARK 3 ORIGIN FOR THE GROUP (A): 44.6418 -17.8414 -36.5612 REMARK 3 T TENSOR REMARK 3 T11: 0.0593 T22: 0.0572 REMARK 3 T33: 0.0890 T12: 0.0210 REMARK 3 T13: -0.0004 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 1.6064 L22: 2.0561 REMARK 3 L33: 1.7981 L12: -0.1573 REMARK 3 L13: -0.2083 L23: 0.6624 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: 0.0861 S13: -0.0288 REMARK 3 S21: -0.0892 S22: -0.0035 S23: -0.2159 REMARK 3 S31: 0.0478 S32: 0.0715 S33: 0.0067 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN B AND RESID 250:294) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5657 -11.1397 -19.0342 REMARK 3 T TENSOR REMARK 3 T11: 0.0633 T22: 0.0760 REMARK 3 T33: 0.0910 T12: 0.0179 REMARK 3 T13: 0.0117 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.0220 L22: 1.5568 REMARK 3 L33: 1.4677 L12: 0.0965 REMARK 3 L13: 0.0863 L23: -0.2626 REMARK 3 S TENSOR REMARK 3 S11: -0.0977 S12: -0.0332 S13: -0.0463 REMARK 3 S21: -0.0214 S22: 0.0237 S23: 0.0626 REMARK 3 S31: 0.0518 S32: -0.0917 S33: 0.0575 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 4KCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : DOUBLE CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72079 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.900 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: 2RC7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 6K, 0.1 M MES, 0.12 M NACL, PH REMARK 280 5.4, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 37.51450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.56950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.94250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.56950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.51450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.94250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER BUT THIS CAN NOT BE REMARK 300 GENERATED BY CRYSTAL SYMMETRY OPERATIONS FOR THIS STRUCTURE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 293 REMARK 465 LYS A 294 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ASP A 235 HH22 ARG B 198 3654 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS B 35 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 14 111.56 -160.12 REMARK 500 THR A 122 -170.06 -172.86 REMARK 500 THR A 143 -154.08 -148.35 REMARK 500 ALA A 248 70.46 59.95 REMARK 500 TYR A 287 59.74 -115.83 REMARK 500 THR B 122 -169.61 -174.36 REMARK 500 ALA B 248 160.88 69.77 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 GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RC7 RELATED DB: PDB REMARK 900 GLUN3A LBD GLYCINE COMPLEX REMARK 900 RELATED ID: 2RC8 RELATED DB: PDB REMARK 900 GLUN3A LBD D-SERINE COMPLEX REMARK 900 RELATED ID: 2RC9 RELATED DB: PDB REMARK 900 GLUN3A LBD ACPC COMPLEX REMARK 900 RELATED ID: 4KCC RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN REMARK 999 OF GLUN3A. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REMARK 999 REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES REMARK 999 DISCONTINUOUSLY WITH THE REFERENCE DATABASE (511-660 AND 776-915). DBREF 4KCD A 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 4KCD A 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 DBREF 4KCD B 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 4KCD B 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 SEQADV 4KCD GLY A 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 4KCD SER A 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 4KCD GLY A 153 UNP Q9R1M7 LINKER SEQADV 4KCD THR A 154 UNP Q9R1M7 LINKER SEQADV 4KCD GLY B 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 4KCD SER B 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 4KCD GLY B 153 UNP Q9R1M7 LINKER SEQADV 4KCD THR B 154 UNP Q9R1M7 LINKER SEQRES 1 A 294 GLY SER ASN LYS LEU HIS LEU ARG VAL VAL THR LEU ILE SEQRES 2 A 294 GLU HIS PRO PHE VAL PHE THR ARG GLU VAL ASP ASP GLU SEQRES 3 A 294 GLY LEU CYS PRO ALA GLY GLN LEU CYS LEU ASP PRO MET SEQRES 4 A 294 THR ASN ASP SER SER MET LEU ASP ARG LEU PHE SER SER SEQRES 5 A 294 LEU HIS SER SER ASN ASP THR VAL PRO ILE LYS PHE LYS SEQRES 6 A 294 LYS CYS CYS TYR GLY TYR CYS ILE ASP LEU LEU GLU GLN SEQRES 7 A 294 LEU ALA GLU ASP MET ASN PHE ASP PHE ASP LEU TYR ILE SEQRES 8 A 294 VAL GLY ASP GLY LYS TYR GLY ALA TRP LYS ASN GLY HIS SEQRES 9 A 294 TRP THR GLY LEU VAL GLY ASP LEU LEU SER GLY THR ALA SEQRES 10 A 294 ASN MET ALA VAL THR SER PHE SER ILE ASN THR ALA ARG SEQRES 11 A 294 SER GLN VAL ILE ASP PHE THR SER PRO PHE PHE SER THR SEQRES 12 A 294 SER LEU GLY ILE LEU VAL ARG THR ARG GLY THR GLU LEU SEQRES 13 A 294 SER GLY ILE HIS ASP PRO LYS LEU HIS HIS PRO SER GLN SEQRES 14 A 294 GLY PHE ARG PHE GLY THR VAL ARG GLU SER SER ALA GLU SEQRES 15 A 294 ASP TYR VAL ARG GLN SER PHE PRO GLU MET HIS GLU TYR SEQRES 16 A 294 MET ARG ARG TYR ASN VAL PRO ALA THR PRO ASP GLY VAL SEQRES 17 A 294 GLN TYR LEU LYS ASN ASP PRO GLU LYS LEU ASP ALA PHE SEQRES 18 A 294 ILE MET ASP LYS ALA LEU LEU ASP TYR GLU VAL SER ILE SEQRES 19 A 294 ASP ALA ASP CYS LYS LEU LEU THR VAL GLY LYS PRO PHE SEQRES 20 A 294 ALA ILE GLU GLY TYR GLY ILE GLY LEU PRO PRO ASN SER SEQRES 21 A 294 PRO LEU THR SER ASN ILE SER GLU LEU ILE SER GLN TYR SEQRES 22 A 294 LYS SER HIS GLY PHE MET ASP VAL LEU HIS ASP LYS TRP SEQRES 23 A 294 TYR LYS VAL VAL PRO CYS GLY LYS SEQRES 1 B 294 GLY SER ASN LYS LEU HIS LEU ARG VAL VAL THR LEU ILE SEQRES 2 B 294 GLU HIS PRO PHE VAL PHE THR ARG GLU VAL ASP ASP GLU SEQRES 3 B 294 GLY LEU CYS PRO ALA GLY GLN LEU CYS LEU ASP PRO MET SEQRES 4 B 294 THR ASN ASP SER SER MET LEU ASP ARG LEU PHE SER SER SEQRES 5 B 294 LEU HIS SER SER ASN ASP THR VAL PRO ILE LYS PHE LYS SEQRES 6 B 294 LYS CYS CYS TYR GLY TYR CYS ILE ASP LEU LEU GLU GLN SEQRES 7 B 294 LEU ALA GLU ASP MET ASN PHE ASP PHE ASP LEU TYR ILE SEQRES 8 B 294 VAL GLY ASP GLY LYS TYR GLY ALA TRP LYS ASN GLY HIS SEQRES 9 B 294 TRP THR GLY LEU VAL GLY ASP LEU LEU SER GLY THR ALA SEQRES 10 B 294 ASN MET ALA VAL THR SER PHE SER ILE ASN THR ALA ARG SEQRES 11 B 294 SER GLN VAL ILE ASP PHE THR SER PRO PHE PHE SER THR SEQRES 12 B 294 SER LEU GLY ILE LEU VAL ARG THR ARG GLY THR GLU LEU SEQRES 13 B 294 SER GLY ILE HIS ASP PRO LYS LEU HIS HIS PRO SER GLN SEQRES 14 B 294 GLY PHE ARG PHE GLY THR VAL ARG GLU SER SER ALA GLU SEQRES 15 B 294 ASP TYR VAL ARG GLN SER PHE PRO GLU MET HIS GLU TYR SEQRES 16 B 294 MET ARG ARG TYR ASN VAL PRO ALA THR PRO ASP GLY VAL SEQRES 17 B 294 GLN TYR LEU LYS ASN ASP PRO GLU LYS LEU ASP ALA PHE SEQRES 18 B 294 ILE MET ASP LYS ALA LEU LEU ASP TYR GLU VAL SER ILE SEQRES 19 B 294 ASP ALA ASP CYS LYS LEU LEU THR VAL GLY LYS PRO PHE SEQRES 20 B 294 ALA ILE GLU GLY TYR GLY ILE GLY LEU PRO PRO ASN SER SEQRES 21 B 294 PRO LEU THR SER ASN ILE SER GLU LEU ILE SER GLN TYR SEQRES 22 B 294 LYS SER HIS GLY PHE MET ASP VAL LEU HIS ASP LYS TRP SEQRES 23 B 294 TYR LYS VAL VAL PRO CYS GLY LYS HET GOL A 301 14 HET GOL B 301 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *579(H2 O) HELIX 1 1 ASP A 42 HIS A 54 1 13 HELIX 2 2 PRO A 61 LYS A 63 5 3 HELIX 3 3 GLY A 70 ASN A 84 1 15 HELIX 4 4 THR A 106 SER A 114 1 9 HELIX 5 5 ASN A 127 GLN A 132 1 6 HELIX 6 6 ASP A 161 HIS A 166 1 6 HELIX 7 7 SER A 179 PHE A 189 1 11 HELIX 8 8 PHE A 189 ARG A 197 1 9 HELIX 9 9 ALA A 203 ASN A 213 1 11 HELIX 10 10 LYS A 225 ASP A 235 1 11 HELIX 11 11 LEU A 262 HIS A 276 1 15 HELIX 12 12 GLY A 277 TYR A 287 1 11 HELIX 13 13 ASP B 42 HIS B 54 1 13 HELIX 14 14 PRO B 61 LYS B 63 5 3 HELIX 15 15 GLY B 70 ASN B 84 1 15 HELIX 16 16 THR B 106 SER B 114 1 9 HELIX 17 17 ASN B 127 GLN B 132 1 6 HELIX 18 18 ASP B 161 HIS B 165 5 5 HELIX 19 19 HIS B 166 GLY B 170 5 5 HELIX 20 20 SER B 179 PHE B 189 1 11 HELIX 21 21 PHE B 189 ARG B 197 1 9 HELIX 22 22 ARG B 198 ASN B 200 5 3 HELIX 23 23 ALA B 203 ASN B 213 1 11 HELIX 24 24 LYS B 225 ILE B 234 1 10 HELIX 25 25 LEU B 262 HIS B 276 1 15 HELIX 26 26 GLY B 277 TYR B 287 1 11 SHEET 1 A 3 PHE A 85 ILE A 91 0 SHEET 2 A 3 LEU A 5 THR A 11 1 N VAL A 9 O ASP A 88 SHEET 3 A 3 MET A 119 ALA A 120 1 O MET A 119 N VAL A 10 SHEET 1 B 3 PHE A 19 ARG A 21 0 SHEET 2 B 3 LYS A 65 TYR A 69 -1 O TYR A 69 N PHE A 19 SHEET 3 B 3 GLN A 33 LEU A 36 -1 N GLN A 33 O CYS A 68 SHEET 1 C 2 TRP A 100 LYS A 101 0 SHEET 2 C 2 HIS A 104 TRP A 105 -1 O HIS A 104 N LYS A 101 SHEET 1 D 2 ASP A 135 PHE A 136 0 SHEET 2 D 2 GLY A 255 LEU A 256 -1 O LEU A 256 N ASP A 135 SHEET 1 E 4 PHE A 173 GLY A 174 0 SHEET 2 E 4 ALA A 220 ASP A 224 1 O ILE A 222 N GLY A 174 SHEET 3 E 4 PHE A 141 ARG A 150 -1 N LEU A 148 O PHE A 221 SHEET 4 E 4 LEU A 240 TYR A 252 -1 O GLU A 250 N THR A 143 SHEET 1 F 3 PHE B 85 ILE B 91 0 SHEET 2 F 3 LEU B 5 THR B 11 1 N VAL B 9 O ASP B 88 SHEET 3 F 3 MET B 119 ALA B 120 1 O MET B 119 N VAL B 10 SHEET 1 G 3 PHE B 19 ARG B 21 0 SHEET 2 G 3 LYS B 65 TYR B 69 -1 O TYR B 69 N PHE B 19 SHEET 3 G 3 GLN B 33 LEU B 36 -1 N GLN B 33 O CYS B 68 SHEET 1 H 2 TRP B 100 LYS B 101 0 SHEET 2 H 2 HIS B 104 TRP B 105 -1 O HIS B 104 N LYS B 101 SHEET 1 I 2 ASP B 135 PHE B 136 0 SHEET 2 I 2 GLY B 255 LEU B 256 -1 O LEU B 256 N ASP B 135 SHEET 1 J 4 PHE B 173 GLY B 174 0 SHEET 2 J 4 ALA B 220 ASP B 224 1 O ILE B 222 N GLY B 174 SHEET 3 J 4 PHE B 141 ARG B 150 -1 N LEU B 148 O PHE B 221 SHEET 4 J 4 LEU B 240 TYR B 252 -1 O PHE B 247 N LEU B 145 SSBOND 1 CYS A 29 CYS A 67 1555 1555 2.07 SSBOND 2 CYS A 35 CYS A 68 1555 1555 2.16 SSBOND 3 CYS A 238 CYS A 292 1555 1555 2.04 SSBOND 4 CYS B 29 CYS B 67 1555 1555 2.07 SSBOND 5 CYS B 35 CYS B 68 1555 1555 2.16 SSBOND 6 CYS B 238 CYS B 292 1555 1555 2.03 CISPEP 1 HIS A 15 PRO A 16 0 7.70 CISPEP 2 ASP A 214 PRO A 215 0 -5.69 CISPEP 3 HIS B 15 PRO B 16 0 5.86 CISPEP 4 ASP B 214 PRO B 215 0 1.33 SITE 1 AC1 7 PHE A 141 ALA A 226 ASP A 229 HIS A 283 SITE 2 AC1 7 TYR A 287 HOH A 628 HOH A 636 SITE 1 AC2 6 ASP B 74 VAL B 281 LYS B 285 HOH B 604 SITE 2 AC2 6 HOH B 638 HOH B 639 CRYST1 75.029 83.885 99.139 90.00 90.00 90.00 P 21 21 21 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 0.013328 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010087 0.00000