HEADER MEMBRANE PROTEIN 19-SEP-07 2RC8 TITLE CRYSTAL STRUCTURE OF THE NR3A LIGAND BINDING CORE COMPLEX WITH D- TITLE 2 SERINE AT 1.45 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 2RC8 1 SOURCE REVDAT 4 13-JUL-11 2RC8 1 VERSN REVDAT 3 24-FEB-09 2RC8 1 VERSN REVDAT 2 19-AUG-08 2RC8 1 JRNL REVDAT 1 05-AUG-08 2RC8 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 91776 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4839 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4859 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE SET COUNT : 233 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4501 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 633 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) : 13.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.941 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5011 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6847 ; 1.656 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 647 ; 5.041 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;33.622 ;24.440 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 833 ;10.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.471 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 727 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3952 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2387 ; 0.251 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3600 ; 0.320 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 964 ; 0.205 ; 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): 87 ; 0.235 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 57 ; 0.246 ; 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): 3155 ; 1.524 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5045 ; 2.230 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2074 ; 2.006 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1801 ; 3.021 ; 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): -1.5950 42.3520 -5.8850 REMARK 3 T TENSOR REMARK 3 T11: .0066 T22: .0898 REMARK 3 T33: -.0122 T12: .0168 REMARK 3 T13: -.0448 T23: .0247 REMARK 3 L TENSOR REMARK 3 L11: 1.5801 L22: 1.4766 REMARK 3 L33: .7608 L12: .0410 REMARK 3 L13: -.4940 L23: .0673 REMARK 3 S TENSOR REMARK 3 S11: .0629 S12: .3539 S13: .0149 REMARK 3 S21: -.2276 S22: -.0141 S23: .2391 REMARK 3 S31: -.0317 S32: -.1966 S33: -.0489 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): 15.4420 53.1780 7.2620 REMARK 3 T TENSOR REMARK 3 T11: .0400 T22: .0134 REMARK 3 T33: .0390 T12: .0061 REMARK 3 T13: -.0014 T23: .0196 REMARK 3 L TENSOR REMARK 3 L11: 1.0779 L22: .8133 REMARK 3 L33: .2951 L12: .1315 REMARK 3 L13: -.0966 L23: -.2134 REMARK 3 S TENSOR REMARK 3 S11: .0128 S12: .0618 S13: .1900 REMARK 3 S21: .0559 S22: -.0127 S23: -.0406 REMARK 3 S31: -.0764 S32: -.0171 S33: -.0002 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): 15.1450 36.2960 4.5030 REMARK 3 T TENSOR REMARK 3 T11: .0392 T22: .0582 REMARK 3 T33: .0312 T12: .0080 REMARK 3 T13: .0021 T23: .0121 REMARK 3 L TENSOR REMARK 3 L11: .5519 L22: .8581 REMARK 3 L33: .2040 L12: -.1463 REMARK 3 L13: .0765 L23: .0184 REMARK 3 S TENSOR REMARK 3 S11: .0168 S12: .0380 S13: -.0470 REMARK 3 S21: -.0254 S22: -.0705 S23: -.0203 REMARK 3 S31: .0198 S32: .0207 S33: .0536 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): 37.5500 26.6580 25.4060 REMARK 3 T TENSOR REMARK 3 T11: .0161 T22: .0343 REMARK 3 T33: .0309 T12: .0160 REMARK 3 T13: .0008 T23: .0342 REMARK 3 L TENSOR REMARK 3 L11: 1.8531 L22: .8678 REMARK 3 L33: .8764 L12: -.0960 REMARK 3 L13: -.1864 L23: .3521 REMARK 3 S TENSOR REMARK 3 S11: -.0927 S12: -.1729 S13: -.2401 REMARK 3 S21: .0901 S22: .0436 S23: -.0964 REMARK 3 S31: .0811 S32: .1491 S33: .0490 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): 15.6920 38.7870 34.3290 REMARK 3 T TENSOR REMARK 3 T11: .0429 T22: .0423 REMARK 3 T33: .0053 T12: .0068 REMARK 3 T13: -.0095 T23: -.0028 REMARK 3 L TENSOR REMARK 3 L11: .9699 L22: .1317 REMARK 3 L33: 1.1756 L12: -.1114 REMARK 3 L13: -.7650 L23: .0637 REMARK 3 S TENSOR REMARK 3 S11: -.0147 S12: -.1037 S13: .0252 REMARK 3 S21: .0474 S22: .0248 S23: -.0189 REMARK 3 S31: -.0250 S32: .0333 S33: -.0100 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): 21.6520 28.3400 17.9820 REMARK 3 T TENSOR REMARK 3 T11: .0466 T22: .0449 REMARK 3 T33: .0639 T12: -.0173 REMARK 3 T13: .0090 T23: -.0067 REMARK 3 L TENSOR REMARK 3 L11: .2978 L22: .2421 REMARK 3 L33: .7590 L12: -.1724 REMARK 3 L13: -.1542 L23: .2324 REMARK 3 S TENSOR REMARK 3 S11: -.0529 S12: .0937 S13: -.0970 REMARK 3 S21: .0130 S22: .0054 S23: .0154 REMARK 3 S31: .0493 S32: -.0830 S33: .0476 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 2RC8 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_1000044685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 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 : 100689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M NASCN, 0.1M NACITRATE, 0.01 M REMARK 280 EDTA, 11% PEG 3350, PH 5.3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 48.85050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2620 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 OE1 GLU B 268 O HOH B 575 2.02 REMARK 500 OD1 ASP B 42 O HOH B 564 2.07 REMARK 500 OE2 GLU B 268 O HOH B 601 2.08 REMARK 500 OE2 GLU B 194 O HOH B 436 2.16 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 PHE B 124 CB - CG - CD2 ANGL. DEV. = -4.3 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 THR A 122 -168.10 -175.32 REMARK 500 THR B 122 -166.27 -177.31 REMARK 500 ASP B 237 30.14 -82.48 REMARK 500 CYS B 238 52.76 35.31 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 CL A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 904 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RC7 RELATED DB: PDB REMARK 900 NR3A COMPLEX WITH GLYCINE 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 900 RELATED ID: 1PB8 RELATED DB: PDB REMARK 900 NR1 COMPLEX WITH D-SERINE 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 2RC8 A 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 2RC8 B 3 152 UNP Q9R1M7 NMD3A_RAT 511 660 DBREF 2RC8 A 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 DBREF 2RC8 B 155 294 UNP Q9R1M7 NMD3A_RAT 776 915 SEQADV 2RC8 GLY A 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC8 SER A 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC8 GLY A 153 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RC8 THR A 154 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RC8 GLY B 1 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC8 SER B 2 UNP Q9R1M7 EXPRESSION TAG SEQADV 2RC8 GLY B 153 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RC8 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 CL A 295 1 HET CL A 296 1 HET DSN A 901 7 HET DSN A 902 7 HET GOL A 903 6 HET GOL A 904 6 HET CL B 295 1 HET GOL B 296 6 HETNAM CL CHLORIDE ION HETNAM DSN D-SERINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CL 3(CL 1-) FORMUL 5 DSN 2(C3 H7 N O3) FORMUL 7 GOL 3(C3 H8 O3) FORMUL 11 HOH *633(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 PRO A 261 HIS A 276 1 16 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 165 5 5 HELIX 20 20 HIS B 166 GLY B 170 5 5 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 ARG B 198 ASN B 200 5 3 HELIX 24 24 ALA B 203 ASN B 213 1 11 HELIX 25 25 LYS B 225 ILE B 234 1 10 HELIX 26 26 PRO B 261 HIS B 276 1 16 HELIX 27 27 GLY B 277 LYS B 288 1 12 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 2.06 SSBOND 2 CYS A 35 CYS A 68 1555 1555 2.20 SSBOND 3 CYS B 29 CYS B 67 1555 1555 2.05 SSBOND 4 CYS B 35 CYS B 68 1555 1555 2.26 CISPEP 1 HIS A 15 PRO A 16 0 -0.06 CISPEP 2 ASP A 214 PRO A 215 0 0.51 CISPEP 3 HIS B 15 PRO B 16 0 2.62 CISPEP 4 ASP B 214 PRO B 215 0 -7.23 CISPEP 5 ASP B 214 PRO B 215 0 2.99 SITE 1 AC1 5 ARG A 21 ALA A 31 CYS A 67 HOH A1143 SITE 2 AC1 5 HOH A1210 SITE 1 AC2 10 TYR A 97 SER A 123 SER A 125 ARG A 130 SITE 2 AC2 10 SER A 179 SER A 180 ALA A 181 MET A 223 SITE 3 AC2 10 ASP A 224 TYR A 252 SITE 1 AC3 11 TYR B 97 SER B 123 PHE B 124 SER B 125 SITE 2 AC3 11 ARG B 130 SER B 179 SER B 180 ALA B 181 SITE 3 AC3 11 MET B 223 ASP B 224 TYR B 252 SITE 1 AC4 6 PRO A 258 ASN A 259 HOH A 992 PRO B 258 SITE 2 AC4 6 HOH B 369 HOH B 516 SITE 1 AC5 7 ASP A 74 LYS A 285 HOH A 943 HOH A 991 SITE 2 AC5 7 HOH A1154 ASP B 214 PRO B 215 SITE 1 AC6 7 GLY A 115 PRO A 258 HOH A1010 HOH A1070 SITE 2 AC6 7 PRO B 258 ASN B 259 HOH B 609 CRYST1 49.790 97.701 60.050 90.00 93.60 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 0.020084 0.000000 0.001262 0.00000 SCALE2 0.000000 0.010235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016686 0.00000