PDB Short entry for 2RC7 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 6 30-AUG-23 2RC7 1 REMARK SEQADV 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,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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