HEADER MEMBRANE PROTEIN 19-SEP-07 2RC7 TITLE CRYSTAL STRUCTURE OF THE NR3A LIGAND BINDING CORE COMPLEX WITH GLYCINE TITLE 2 AT 1.58 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE [NMDA] RECEPTOR SUBUNIT 3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 511-660, 776-915; COMPND 5 SYNONYM: N-METHYL-D-ASPARTATE RECEPTOR SUBTYPE 3A, NR3A, NMDAR-L, COMPND 6 NMDAR-L1, N-METHYL-D-ASPARTATE RECEPTOR, CHI-1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 GENE: GRIN3A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ORIGAMIB (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B(+) MODIFIED; SOURCE 9 OTHER_DETAILS: PEPTIDES CORRESPONDING TO N511-R660 AND E776-K915 SOURCE 10 WERE COUPLED BY A GT DIPEPTID E SYNTHETIC LINKER KEYWDS MEMBRANE PROTEIN, CELL JUNCTION, GLYCOPROTEIN, ION TRANSPORT, IONIC KEYWDS 2 CHANNEL, MAGNESIUM, POSTSYNAPTIC CELL MEMBRANE, RECEPTOR, SYNAPSE, KEYWDS 3 TRANSMEMBRANE, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAO,M.L.MAYER REVDAT 5 23-AUG-17 2RC7 1 SOURCE REVDAT 4 13-JUL-11 2RC7 1 VERSN REVDAT 3 24-FEB-09 2RC7 1 VERSN REVDAT 2 19-AUG-08 2RC7 1 JRNL REVDAT 1 05-AUG-08 2RC7 0 JRNL AUTH Y.YAO,C.B.HARRISON,P.L.FREDDOLINO,K.SCHULTEN,M.L.MAYER JRNL TITL MOLECULAR MECHANISM OF LIGAND RECOGNITION BY NR3 SUBTYPE JRNL TITL 2 GLUTAMATE RECEPTORS. JRNL REF EMBO J. V. 27 2158 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 18636091 JRNL DOI 10.1038/EMBOJ.2008.140 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.YAO,M.L.MAYER REMARK 1 TITL CHARACTERIZATION OF A SOLUBLE LIGAND BINDING DOMAIN OF THE REMARK 1 TITL 2 NMDA RECEPTOR REGULATORY SUBUNIT NR3A REMARK 1 REF J.NEUROSCI. V. 26 4559 2006 REMARK 1 REFN ISSN 0270-6474 REMARK 1 PMID 16641235 REMARK 1 DOI 10.1523/JNEUROSCI.0560-06.2006 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0038 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 71208 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 + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3768 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3935 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.1630 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 631 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.520 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5108 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6990 ; 1.460 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 668 ; 5.004 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 240 ;34.517 ;24.458 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 849 ;11.247 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;18.550 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 734 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4070 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2462 ; 0.248 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3674 ; 0.320 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 1032 ; 0.200 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 72 ; 0.246 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 64 ; 0.175 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3213 ; 1.287 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5155 ; 1.928 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2114 ; 1.594 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1835 ; 2.385 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 84 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0900 42.0610 -5.9900 REMARK 3 T TENSOR REMARK 3 T11: -.0059 T22: .0525 REMARK 3 T33: -.0273 T12: .0208 REMARK 3 T13: -.0386 T23: .0143 REMARK 3 L TENSOR REMARK 3 L11: 1.4483 L22: 1.4833 REMARK 3 L33: 1.1617 L12: .1294 REMARK 3 L13: -.4043 L23: .0519 REMARK 3 S TENSOR REMARK 3 S11: .0637 S12: .2838 S13: .0260 REMARK 3 S21: -.1801 S22: -.0259 S23: .2390 REMARK 3 S31: -.0511 S32: -.2097 S33: -.0377 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 85 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): 15.6050 53.5530 7.6660 REMARK 3 T TENSOR REMARK 3 T11: .0358 T22: .0020 REMARK 3 T33: .0326 T12: .0026 REMARK 3 T13: -.0009 T23: .0117 REMARK 3 L TENSOR REMARK 3 L11: 1.0116 L22: .6175 REMARK 3 L33: .3409 L12: .0733 REMARK 3 L13: -.1023 L23: -.2075 REMARK 3 S TENSOR REMARK 3 S11: .0229 S12: .0314 S13: .1779 REMARK 3 S21: .0293 S22: -.0286 S23: -.0557 REMARK 3 S31: -.0779 S32: -.0106 S33: .0057 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 234 A 287 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2150 36.2680 4.3910 REMARK 3 T TENSOR REMARK 3 T11: .0330 T22: .0306 REMARK 3 T33: .0186 T12: .0052 REMARK 3 T13: -.0026 T23: .0108 REMARK 3 L TENSOR REMARK 3 L11: .6697 L22: .5810 REMARK 3 L33: .4116 L12: -.2001 REMARK 3 L13: .0655 L23: .0490 REMARK 3 S TENSOR REMARK 3 S11: .0141 S12: .0551 S13: -.0258 REMARK 3 S21: -.0463 S22: -.0696 S23: -.0374 REMARK 3 S31: .0299 S32: .0213 S33: .0554 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 55 REMARK 3 ORIGIN FOR THE GROUP (A): 40.1300 22.5250 27.9680 REMARK 3 T TENSOR REMARK 3 T11: -.0047 T22: -.0044 REMARK 3 T33: .0216 T12: .0358 REMARK 3 T13: -.0075 T23: .0412 REMARK 3 L TENSOR REMARK 3 L11: 1.8196 L22: 1.3453 REMARK 3 L33: 1.1695 L12: .2818 REMARK 3 L13: -.0680 L23: .3183 REMARK 3 S TENSOR REMARK 3 S11: -.0658 S12: -.1928 S13: -.3248 REMARK 3 S21: .1350 S22: .0696 S23: -.1876 REMARK 3 S31: .1503 S32: .2018 S33: -.0037 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 56 B 230 REMARK 3 ORIGIN FOR THE GROUP (A): 24.8250 35.3420 29.7520 REMARK 3 T TENSOR REMARK 3 T11: .0539 T22: .0445 REMARK 3 T33: .0255 T12: .0004 REMARK 3 T13: -.0124 T23: .0033 REMARK 3 L TENSOR REMARK 3 L11: 1.0073 L22: .1700 REMARK 3 L33: .5742 L12: -.0876 REMARK 3 L13: -.4783 L23: .0522 REMARK 3 S TENSOR REMARK 3 S11: -.0364 S12: -.1076 S13: -.0330 REMARK 3 S21: .0366 S22: .0163 S23: -.0309 REMARK 3 S31: .0036 S32: .0566 S33: .0200 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 231 B 287 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3770 28.5310 17.5850 REMARK 3 T TENSOR REMARK 3 T11: .0395 T22: .0327 REMARK 3 T33: .0464 T12: -.0167 REMARK 3 T13: .0017 T23: -.0082 REMARK 3 L TENSOR REMARK 3 L11: .4390 L22: .3610 REMARK 3 L33: .5772 L12: -.2423 REMARK 3 L13: -.1601 L23: .1858 REMARK 3 S TENSOR REMARK 3 S11: -.0503 S12: .0677 S13: -.1137 REMARK 3 S21: .0052 S22: .0146 S23: .0319 REMARK 3 S31: .0556 S32: -.0726 S33: .0358 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2RC7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000044684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 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) : 0.97931 REMARK 200 MONOCHROMATOR : SI 220 REMARK 200 OPTICS : NULL 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 : 74941 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 95.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.20900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 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 1PB7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NABR, 0.1 MM NAACETATE, 4% PEG REMARK 280 4000, PH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 48.78400 REMARK 290 SMTRY3 2 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 UNIT IS BELIEVED TO BE A DIMER OF DIMERS. REMARK 300 MOLECULAR PACKING IN THE PRESENT STRUCTURE IS NOT BIOLOGICALLY REMARK 300 RELEVANT. 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 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 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 ASN A 3 REMARK 465 LYS A 288 REMARK 465 VAL A 289 REMARK 465 VAL A 290 REMARK 465 PRO A 291 REMARK 465 CYS A 292 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 465 LYS B 288 REMARK 465 VAL B 289 REMARK 465 VAL B 290 REMARK 465 PRO B 291 REMARK 465 CYS B 292 REMARK 465 GLY B 293 REMARK 465 LYS B 294 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O1 GOL A 302 O HOH A 471 1.94 REMARK 500 NZ LYS A 239 O HOH A 524 2.08 REMARK 500 OD1 ASP B 183 O HOH B 1121 2.10 REMARK 500 OD1 ASP A 280 O HOH A 546 2.11 REMARK 500 O HOH B 1088 O HOH B 1199 2.14 REMARK 500 O HOH B 1121 O HOH B 1193 2.18 REMARK 500 O HOH A 427 O HOH A 616 2.19 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 26 39.73 -91.09 REMARK 500 ASN A 57 56.33 -111.86 REMARK 500 THR A 122 -166.85 -175.47 REMARK 500 ASP B 25 5.41 -69.54 REMARK 500 THR B 122 -164.52 -173.30 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 BR A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RC8 RELATED DB: PDB REMARK 900 NR3A COMPLEX WITH D-SERINE REMARK 900 RELATED ID: 2RC9 RELATED DB: PDB REMARK 900 NR3A COMPLEX WITH ACPC REMARK 900 RELATED ID: 2RCA RELATED DB: PDB REMARK 900 NR3B COMPLEX WITH GLYCINE REMARK 900 RELATED ID: 2RCB RELATED DB: PDB REMARK 900 NR3B COMPLEX WITH D-SERINE REMARK 900 RELATED ID: 1PB7 RELATED DB: PDB REMARK 900 NR1 COMPLEX WITH GLYCINE REMARK 999 REMARK 999 RESIDUES 153 AND 154, GLY AND THR, ARE INSERTED AS A REMARK 999 LINK REPLACING RESIDUES 661-775 OF THE PROTEIN FROM REMARK 999 THE UNP ENTRY Q9R1M7 DBREF 2RC7 A 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 2RC7 B 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 2RC7 A 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 DBREF 2RC7 B 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 SEQADV 2RC7 GLY A 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC7 SER A 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC7 GLY A 153 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RC7 THR A 154 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RC7 GLY B 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC7 SER B 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC7 GLY B 153 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RC7 THR B 154 UNP Q9R1M7 SEE REMARK 999 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 BR A 295 1 HET CL A 296 1 HET CL A 297 1 HET CL A 298 1 HET CL A 299 1 HET GOL A 300 6 HET GOL A 301 6 HET GOL A 302 6 HET CL B 295 1 HET CL B 296 1 HET CL B 297 1 HET GLY B 901 5 HET GLY B 902 5 HET GOL B 903 6 HETNAM BR BROMIDE ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM GLY GLYCINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 BR BR 1- FORMUL 4 CL 7(CL 1-) FORMUL 8 GOL 4(C3 H8 O3) FORMUL 14 GLY 2(C2 H5 N O2) FORMUL 17 HOH *631(H2 O) HELIX 1 1 ASP A 42 SER A 55 1 14 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 ARG A 198 ASN A 200 5 3 HELIX 10 10 ALA A 203 ASN A 213 1 11 HELIX 11 11 LYS A 225 ILE A 234 1 10 HELIX 12 12 LEU A 262 HIS A 276 1 15 HELIX 13 13 GLY A 277 TYR A 287 1 11 HELIX 14 14 ASP B 42 HIS B 54 1 13 HELIX 15 15 PRO B 61 LYS B 63 5 3 HELIX 16 16 GLY B 70 MET B 83 1 14 HELIX 17 17 THR B 106 SER B 114 1 9 HELIX 18 18 ASN B 127 GLN B 132 1 6 HELIX 19 19 ASP B 161 HIS B 166 1 6 HELIX 20 20 PRO B 167 GLY B 170 5 4 HELIX 21 21 SER B 179 PHE B 189 1 11 HELIX 22 22 PHE B 189 ARG B 197 1 9 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 CYS A 67 N ARG A 21 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 THR A 242 -1 O LEU A 241 N VAL A 149 SHEET 1 F 4 PHE A 173 GLY A 174 0 SHEET 2 F 4 ALA A 220 ASP A 224 1 O ILE A 222 N GLY A 174 SHEET 3 F 4 PHE A 141 ARG A 150 -1 N LEU A 148 O PHE A 221 SHEET 4 F 4 PHE A 247 TYR A 252 -1 O PHE A 247 N LEU A 145 SHEET 1 G 3 PHE B 85 ILE B 91 0 SHEET 2 G 3 LEU B 5 THR B 11 1 N VAL B 9 O ASP B 88 SHEET 3 G 3 MET B 119 ALA B 120 1 O MET B 119 N VAL B 10 SHEET 1 H 3 PHE B 19 GLU B 22 0 SHEET 2 H 3 LYS B 65 TYR B 69 -1 O TYR B 69 N PHE B 19 SHEET 3 H 3 GLN B 33 LEU B 36 -1 N GLN B 33 O CYS B 68 SHEET 1 I 2 TRP B 100 LYS B 101 0 SHEET 2 I 2 HIS B 104 TRP B 105 -1 O HIS B 104 N LYS B 101 SHEET 1 J 2 ASP B 135 PHE B 136 0 SHEET 2 J 2 GLY B 255 LEU B 256 -1 O LEU B 256 N ASP B 135 SHEET 1 K 4 PHE B 173 GLY B 174 0 SHEET 2 K 4 ALA B 220 ASP B 224 1 O ILE B 222 N GLY B 174 SHEET 3 K 4 PHE B 141 ARG B 150 -1 N LEU B 148 O PHE B 221 SHEET 4 K 4 LEU B 240 THR B 242 -1 O LEU B 241 N VAL B 149 SHEET 1 L 4 PHE B 173 GLY B 174 0 SHEET 2 L 4 ALA B 220 ASP B 224 1 O ILE B 222 N GLY B 174 SHEET 3 L 4 PHE B 141 ARG B 150 -1 N LEU B 148 O PHE B 221 SHEET 4 L 4 PHE B 247 TYR B 252 -1 O PHE B 247 N LEU B 145 SSBOND 1 CYS A 29 CYS A 67 1555 1555 2.03 SSBOND 2 CYS A 35 CYS A 68 1555 1555 2.08 SSBOND 3 CYS B 29 CYS B 67 1555 1555 2.05 SSBOND 4 CYS B 35 CYS B 68 1555 1555 2.03 CISPEP 1 HIS A 15 PRO A 16 0 -1.02 CISPEP 2 ASP A 214 PRO A 215 0 1.62 CISPEP 3 HIS B 15 PRO B 16 0 1.95 CISPEP 4 ASP B 214 PRO B 215 0 1.65 CISPEP 5 ASP B 214 PRO B 215 0 -6.05 SITE 1 AC1 3 ARG A 21 ALA A 31 GLY A 32 SITE 1 AC2 3 ARG A 21 ALA A 31 HOH A 400 SITE 1 AC3 6 ARG B 21 CYS B 29 PRO B 30 ALA B 31 SITE 2 AC3 6 CYS B 67 HOH B1002 SITE 1 AC4 3 MET B 45 PHE B 64 ARG B 152 SITE 1 AC5 3 LYS A 96 ARG A 177 PRO A 202 SITE 1 AC6 3 MET A 45 PHE A 64 ARG A 152 SITE 1 AC7 8 TYR A 97 SER A 123 PHE A 124 SER A 125 SITE 2 AC7 8 ARG A 130 SER A 179 SER A 180 ASP A 224 SITE 1 AC8 7 TYR B 97 SER B 123 SER B 125 ARG B 130 SITE 2 AC8 7 SER B 179 SER B 180 ASP B 224 SITE 1 AC9 9 LEU A 112 LEU A 113 GLY A 115 PRO A 258 SITE 2 AC9 9 HOH A 363 HOH A 475 PRO B 258 ASN B 259 SITE 3 AC9 9 HOH B 967 SITE 1 BC1 8 PRO A 258 ASN A 259 HOH A 332 LEU B 112 SITE 2 BC1 8 LEU B 113 PRO B 258 HOH B 951 HOH B1032 SITE 1 BC2 8 ASP A 74 LYS A 285 HOH A 328 HOH A 533 SITE 2 BC2 8 HOH A 556 ASP B 214 PRO B 215 HOH B1011 SITE 1 BC3 6 HIS A 165 PHE A 189 PRO A 190 GLU A 191 SITE 2 BC3 6 MET A 192 HOH A 471 CRYST1 49.892 97.568 59.901 90.00 93.55 90.00 P 1 21 1 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 0.020043 0.000000 0.001244 0.00000 SCALE2 0.000000 0.010249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016726 0.00000 MASTER 485 0 14 26 36 0 20 6 0 0 0 46 END