HEADER MEMBRANE PROTEIN 19-SEP-07 2RC9 TITLE CRYSTAL STRUCTURE OF THE NR3A LIGAND BINDING CORE COMPLEX WITH ACPC AT TITLE 2 1.96 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 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GRIN3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMIB (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+) MODIFIED; SOURCE 11 OTHER_DETAILS: PEPTIDES CORRESPONDING TO N511-R660 AND E776-K915 SOURCE 12 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 7 30-AUG-23 2RC9 1 REMARK SEQADV REVDAT 6 23-AUG-17 2RC9 1 SOURCE REVDAT 5 13-JUL-11 2RC9 1 VERSN REVDAT 4 14-APR-10 2RC9 1 DBREF SEQADV REVDAT 3 24-FEB-09 2RC9 1 VERSN REVDAT 2 19-AUG-08 2RC9 1 JRNL REVDAT 1 05-AUG-08 2RC9 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 40128 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2106 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2893 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4524 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 513 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) : 14.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00000 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): 0.163 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.756 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4816 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6559 ; 1.450 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 605 ; 6.089 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 221 ;34.757 ;24.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 802 ;13.966 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.032 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 706 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3727 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2244 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3376 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 470 ; 0.154 ; 0.200 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): 66 ; 0.211 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.280 ; 0.200 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): 3030 ; 0.861 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4801 ; 1.383 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2021 ; 2.241 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1752 ; 3.513 ; 4.500 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 : 8 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 82 REMARK 3 ORIGIN FOR THE GROUP (A): -1.5630 -3.2490 -6.6370 REMARK 3 T TENSOR REMARK 3 T11: -.0002 T22: .0485 REMARK 3 T33: -.0075 T12: -.0043 REMARK 3 T13: -.0511 T23: .0242 REMARK 3 L TENSOR REMARK 3 L11: 2.4265 L22: 1.9257 REMARK 3 L33: .5370 L12: -.4127 REMARK 3 L13: -.2607 L23: .0256 REMARK 3 S TENSOR REMARK 3 S11: -.0030 S12: .3913 S13: .1167 REMARK 3 S21: -.2736 S22: .0115 S23: .3369 REMARK 3 S31: -.0124 S32: -.1384 S33: -.0085 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 83 A 181 REMARK 3 ORIGIN FOR THE GROUP (A): 12.3890 2.9940 8.9200 REMARK 3 T TENSOR REMARK 3 T11: .0516 T22: -.0048 REMARK 3 T33: .0330 T12: .0092 REMARK 3 T13: .0052 T23: -.0135 REMARK 3 L TENSOR REMARK 3 L11: 1.9252 L22: .7906 REMARK 3 L33: .6267 L12: .2440 REMARK 3 L13: .1666 L23: -.1526 REMARK 3 S TENSOR REMARK 3 S11: .0067 S12: -.0085 S13: .2146 REMARK 3 S21: .0719 S22: -.0078 S23: .0142 REMARK 3 S31: -.0934 S32: -.0117 S33: .0011 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 182 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): 19.1150 12.8870 7.8820 REMARK 3 T TENSOR REMARK 3 T11: .0218 T22: -.0443 REMARK 3 T33: .0826 T12: .0051 REMARK 3 T13: -.0142 T23: -.0055 REMARK 3 L TENSOR REMARK 3 L11: 1.4051 L22: 2.1170 REMARK 3 L33: 3.7147 L12: .0534 REMARK 3 L13: -.2726 L23: -1.2874 REMARK 3 S TENSOR REMARK 3 S11: .0223 S12: .0041 S13: .2602 REMARK 3 S21: .1580 S22: -.0522 S23: .0416 REMARK 3 S31: -.2199 S32: -.1873 S33: .0300 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 : A 224 A 290 REMARK 3 ORIGIN FOR THE GROUP (A): 16.7560 -8.2430 2.0300 REMARK 3 T TENSOR REMARK 3 T11: .0441 T22: .0566 REMARK 3 T33: .0297 T12: .0099 REMARK 3 T13: .0045 T23: -.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.1952 L22: .8712 REMARK 3 L33: .7555 L12: .1467 REMARK 3 L13: .3836 L23: .2652 REMARK 3 S TENSOR REMARK 3 S11: .0013 S12: .1504 S13: -.0055 REMARK 3 S21: -.0728 S22: .0043 S23: -.0862 REMARK 3 S31: -.0108 S32: .0937 S33: -.0056 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 4 B 82 REMARK 3 ORIGIN FOR THE GROUP (A): 38.3730 -28.0410 24.0270 REMARK 3 T TENSOR REMARK 3 T11: .0093 T22: -.0212 REMARK 3 T33: .0458 T12: .0539 REMARK 3 T13: -.0421 T23: .0518 REMARK 3 L TENSOR REMARK 3 L11: 2.0856 L22: .9151 REMARK 3 L33: 1.9910 L12: .4340 REMARK 3 L13: .0467 L23: .8111 REMARK 3 S TENSOR REMARK 3 S11: .0175 S12: -.2582 S13: -.4502 REMARK 3 S21: .2074 S22: .0801 S23: -.2031 REMARK 3 S31: .3630 S32: .3418 S33: -.0977 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 83 B 162 REMARK 3 ORIGIN FOR THE GROUP (A): 27.2080 -12.8470 24.0250 REMARK 3 T TENSOR REMARK 3 T11: .0483 T22: .0316 REMARK 3 T33: .0108 T12: -.0110 REMARK 3 T13: -.0131 T23: .0068 REMARK 3 L TENSOR REMARK 3 L11: 1.6037 L22: .4388 REMARK 3 L33: .9610 L12: -.1386 REMARK 3 L13: -.2435 L23: .2194 REMARK 3 S TENSOR REMARK 3 S11: -.0139 S12: -.1249 S13: -.0375 REMARK 3 S21: .0330 S22: .0013 S23: -.0340 REMARK 3 S31: -.0444 S32: .0266 S33: .0127 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 163 B 221 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0510 -9.1110 37.2600 REMARK 3 T TENSOR REMARK 3 T11: .0462 T22: .0861 REMARK 3 T33: -.0253 T12: -.0163 REMARK 3 T13: -.0074 T23: -.0347 REMARK 3 L TENSOR REMARK 3 L11: 1.4425 L22: .7779 REMARK 3 L33: 2.5055 L12: -.1994 REMARK 3 L13: -.6253 L23: -.1157 REMARK 3 S TENSOR REMARK 3 S11: .0418 S12: -.1402 S13: .0943 REMARK 3 S21: .1209 S22: -.0171 S23: .0107 REMARK 3 S31: -.1159 S32: .0706 S33: -.0246 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 222 B 287 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5580 -19.7200 17.9930 REMARK 3 T TENSOR REMARK 3 T11: .0383 T22: .0374 REMARK 3 T33: .0489 T12: -.0136 REMARK 3 T13: -.0139 T23: .0064 REMARK 3 L TENSOR REMARK 3 L11: .9978 L22: .9237 REMARK 3 L33: .9535 L12: -.2986 REMARK 3 L13: -.3394 L23: .4434 REMARK 3 S TENSOR REMARK 3 S11: -.0318 S12: .0227 S13: -.1699 REMARK 3 S21: .0699 S22: -.0431 S23: .0787 REMARK 3 S31: .0807 S32: -.1087 S33: .0750 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 2RC9 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_1000044686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 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 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 : 43239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 REMARK 200 R SYM FOR SHELL (I) : 0.02590 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2RC7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MG ACETATE, 0.1 M NACITRATE, 14% REMARK 280 PEG 3350, PH 5.7, 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 51.77600 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 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 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 O HOH A 1237 O HOH A 1258 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 SG CYS A 238 O HOH A 1246 1655 2.08 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 THR A 122 -164.44 -175.25 REMARK 500 THR B 122 -166.13 -175.47 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 1AC A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1AC B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RC7 RELATED DB: PDB REMARK 900 NR3A COMPLEX WITH GLYCINE REMARK 900 RELATED ID: 2RC8 RELATED DB: PDB REMARK 900 NR3A COMPLEX WITH D-SERINE 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: 1Y20 RELATED DB: PDB REMARK 900 NR1 COMPLEX WITH ACPC 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 2RC9 A 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 2RC9 A 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 DBREF 2RC9 B 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 2RC9 B 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 SEQADV 2RC9 GLY A 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC9 SER A 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC9 GLY A 153 UNP Q9R1M7 LINKER SEQADV 2RC9 THR A 154 UNP Q9R1M7 LINKER SEQADV 2RC9 GLY B 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC9 SER B 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC9 GLY B 153 UNP Q9R1M7 LINKER SEQADV 2RC9 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 1AC A1001 7 HET 1AC B1002 7 HETNAM 1AC 1-AMINOCYCLOPROPANECARBOXYLIC ACID FORMUL 3 1AC 2(C4 H7 N O2) FORMUL 5 HOH *513(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 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 ASP A 235 1 11 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 SER B 55 1 14 HELIX 15 15 PRO B 61 LYS B 63 5 3 HELIX 16 16 GLY B 70 ASN B 84 1 15 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 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 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 GLY A 146 O MET A 223 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 GLY A 146 O MET A 223 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 ARG B 21 0 SHEET 2 H 3 LYS B 65 TYR B 69 -1 O CYS B 67 N ARG B 21 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 TYR B 252 -1 O PHE B 247 N LEU B 145 SSBOND 1 CYS A 29 CYS A 67 1555 1555 2.06 SSBOND 2 CYS A 35 CYS A 68 1555 1555 2.03 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 1.07 CISPEP 2 ASP A 214 PRO A 215 0 0.51 CISPEP 3 HIS B 15 PRO B 16 0 -0.55 CISPEP 4 ASP B 214 PRO B 215 0 -9.89 SITE 1 AC1 10 TYR A 97 SER A 123 PHE A 124 SER A 125 SITE 2 AC1 10 ARG A 130 SER A 179 SER A 180 MET A 223 SITE 3 AC1 10 ASP A 224 TYR A 252 SITE 1 AC2 9 TYR B 97 SER B 123 SER B 125 ARG B 130 SITE 2 AC2 9 SER B 179 SER B 180 MET B 223 ASP B 224 SITE 3 AC2 9 TYR B 252 CRYST1 49.675 103.552 59.798 90.00 95.04 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 0.020131 0.000000 0.001776 0.00000 SCALE2 0.000000 0.009657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016788 0.00000