HEADER MEMBRANE PROTEIN 19-SEP-07 2RCA TITLE CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WITH GLYCINE TITLE 2 AT 1.58 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE [NMDA] RECEPTOR SUBUNIT 3B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 413-560, 676-815; COMPND 5 SYNONYM: N-METHYL-D-ASPARTATE RECEPTOR SUBTYPE 3B, NR3B, NMDAR3B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 GENE: GRIN3B; 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 A413-R560 AND E676-K815 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 7 30-OCT-24 2RCA 1 REMARK REVDAT 6 30-AUG-23 2RCA 1 REMARK SEQADV REVDAT 5 23-AUG-17 2RCA 1 SOURCE REVDAT 4 13-JUL-11 2RCA 1 VERSN REVDAT 3 24-FEB-09 2RCA 1 VERSN REVDAT 2 19-AUG-08 2RCA 1 JRNL REVDAT 1 05-AUG-08 2RCA 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) : 36.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 65212 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 5502 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) : 1.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4606 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 347 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4390 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 527 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) : 19.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.38000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : -0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.262 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4588 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6233 ; 1.579 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 580 ; 5.057 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;30.267 ;22.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 737 ;11.381 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.780 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 677 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3540 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2113 ; 0.231 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3263 ; 0.316 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 773 ; 0.185 ; 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): 47 ; 0.279 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.229 ; 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): 2933 ; 1.494 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4618 ; 2.081 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1859 ; 1.828 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1615 ; 2.653 ; 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 : 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 113 REMARK 3 ORIGIN FOR THE GROUP (A): 44.7490 27.1540 13.6640 REMARK 3 T TENSOR REMARK 3 T11: .0208 T22: .0500 REMARK 3 T33: .0562 T12: .0123 REMARK 3 T13: .0286 T23: .0042 REMARK 3 L TENSOR REMARK 3 L11: 1.3362 L22: .6652 REMARK 3 L33: 1.1847 L12: .2146 REMARK 3 L13: -.0691 L23: -.2516 REMARK 3 S TENSOR REMARK 3 S11: .0811 S12: .1526 S13: .1214 REMARK 3 S21: -.0114 S22: -.0036 S23: .1127 REMARK 3 S31: -.1490 S32: -.1281 S33: -.0776 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 114 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): 63.7600 19.2830 26.1610 REMARK 3 T TENSOR REMARK 3 T11: .0202 T22: .0911 REMARK 3 T33: .0557 T12: -.0511 REMARK 3 T13: .0021 T23: -.0029 REMARK 3 L TENSOR REMARK 3 L11: .8842 L22: 1.0005 REMARK 3 L33: 1.2315 L12: -.1163 REMARK 3 L13: -.0584 L23: -.3775 REMARK 3 S TENSOR REMARK 3 S11: .0673 S12: -.0943 S13: -.0530 REMARK 3 S21: .0619 S22: -.0754 S23: -.1175 REMARK 3 S31: .0013 S32: .2101 S33: .0082 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 193 A 259 REMARK 3 ORIGIN FOR THE GROUP (A): 57.6790 14.5960 26.6520 REMARK 3 T TENSOR REMARK 3 T11: .0184 T22: .0757 REMARK 3 T33: .0477 T12: -.0351 REMARK 3 T13: -.0015 T23: .0039 REMARK 3 L TENSOR REMARK 3 L11: .6623 L22: 1.9319 REMARK 3 L33: .8989 L12: -.1409 REMARK 3 L13: -.0102 L23: -.3621 REMARK 3 S TENSOR REMARK 3 S11: .0736 S12: -.0677 S13: -.0582 REMARK 3 S21: .0175 S22: -.0375 S23: -.0285 REMARK 3 S31: .0369 S32: .1012 S33: -.0361 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 260 A 285 REMARK 3 ORIGIN FOR THE GROUP (A): 45.9510 34.7960 31.6800 REMARK 3 T TENSOR REMARK 3 T11: .0636 T22: .0255 REMARK 3 T33: .0490 T12: .0025 REMARK 3 T13: .0545 T23: -.0510 REMARK 3 L TENSOR REMARK 3 L11: 1.3220 L22: .8854 REMARK 3 L33: 2.3667 L12: -.5670 REMARK 3 L13: -1.0891 L23: .4487 REMARK 3 S TENSOR REMARK 3 S11: .0768 S12: -.1864 S13: .1965 REMARK 3 S21: .0594 S22: .0442 S23: -.1420 REMARK 3 S31: -.3041 S32: -.0777 S33: -.1210 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 102 REMARK 3 ORIGIN FOR THE GROUP (A): 62.7720 -14.7550 21.9960 REMARK 3 T TENSOR REMARK 3 T11: .0849 T22: .0247 REMARK 3 T33: .0111 T12: .0485 REMARK 3 T13: -.0423 T23: .0289 REMARK 3 L TENSOR REMARK 3 L11: .9930 L22: 1.4970 REMARK 3 L33: .9270 L12: -.2211 REMARK 3 L13: .0930 L23: .2380 REMARK 3 S TENSOR REMARK 3 S11: -.0560 S12: -.0828 S13: -.0085 REMARK 3 S21: .2886 S22: .0149 S23: -.2862 REMARK 3 S31: .0539 S32: .2531 S33: .0411 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 103 B 170 REMARK 3 ORIGIN FOR THE GROUP (A): 49.1570 -8.3510 5.8990 REMARK 3 T TENSOR REMARK 3 T11: .0696 T22: .0439 REMARK 3 T33: .0352 T12: -.0055 REMARK 3 T13: -.0176 T23: -.0006 REMARK 3 L TENSOR REMARK 3 L11: .8641 L22: 1.6087 REMARK 3 L33: .7030 L12: -.6611 REMARK 3 L13: .0591 L23: -.5036 REMARK 3 S TENSOR REMARK 3 S11: -.0126 S12: -.0422 S13: -.0259 REMARK 3 S21: -.1296 S22: .0253 S23: .0540 REMARK 3 S31: .1072 S32: -.0194 S33: -.0128 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 171 B 228 REMARK 3 ORIGIN FOR THE GROUP (A): 47.9590 .5730 6.9700 REMARK 3 T TENSOR REMARK 3 T11: .0723 T22: .0343 REMARK 3 T33: .0224 T12: .0138 REMARK 3 T13: -.0125 T23: .0029 REMARK 3 L TENSOR REMARK 3 L11: .6870 L22: 2.3725 REMARK 3 L33: .1360 L12: -.6730 REMARK 3 L13: -.0153 L23: .0061 REMARK 3 S TENSOR REMARK 3 S11: .0875 S12: .0667 S13: .0462 REMARK 3 S21: -.2518 S22: -.0645 S23: -.0321 REMARK 3 S31: .0798 S32: -.0196 S33: -.0231 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 229 B 285 REMARK 3 ORIGIN FOR THE GROUP (A): 46.8070 -18.5980 14.6020 REMARK 3 T TENSOR REMARK 3 T11: .0430 T22: .0381 REMARK 3 T33: .0495 T12: .0042 REMARK 3 T13: .0337 T23: .0186 REMARK 3 L TENSOR REMARK 3 L11: .8848 L22: 1.9390 REMARK 3 L33: .3469 L12: -.5470 REMARK 3 L13: .2004 L23: -.4086 REMARK 3 S TENSOR REMARK 3 S11: -.0951 S12: -.1936 S13: -.1682 REMARK 3 S21: .0916 S22: .0778 S23: .3333 REMARK 3 S31: .1127 S32: -.0692 S33: .0173 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 2RCA 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_1000044687. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 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) : 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 : 76724 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 92.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 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 (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.250 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 2RCB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NACITRATE, 17% PEG 4000, PH 6.2, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 22.95750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.57650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.79850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.57650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.95750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.79850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL 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 ALA A 3 REMARK 465 LYS A 286 REMARK 465 MET A 287 REMARK 465 VAL A 288 REMARK 465 PRO A 289 REMARK 465 CYS A 290 REMARK 465 GLY A 291 REMARK 465 LYS A 292 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 ALA B 3 REMARK 465 LYS B 286 REMARK 465 MET B 287 REMARK 465 VAL B 288 REMARK 465 PRO B 289 REMARK 465 CYS B 290 REMARK 465 GLY B 291 REMARK 465 LYS B 292 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 ALA B 31 O HOH B 504 1.96 REMARK 500 OG1 THR B 210 O HOH B 405 2.11 REMARK 500 OG1 THR A 210 O HOH A 1122 2.14 REMARK 500 OD2 ASP A 227 O HOH A 1218 2.15 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 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.4 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 120 -165.48 -177.48 REMARK 500 ASN B 55 42.10 -98.25 REMARK 500 THR B 120 -163.96 -174.33 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 GLY A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 903 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RCB RELATED DB: PDB REMARK 900 NR3B COMPLEX WITH D-SERINE 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: 2RC9 RELATED DB: PDB REMARK 900 NR3A COMPLEX WITH ACPC REMARK 900 RELATED ID: 1PB7 RELATED DB: PDB REMARK 900 NR1 COMPLEX WITH GLYCINE REMARK 999 REMARK 999 RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A REMARK 999 LINK REPLACING RESIDUES 561-675 OF THE PROTEIN FROM REMARK 999 THE UNP ENTRY Q8VHN2 DBREF 2RCA A 3 150 UNP Q8VHN2 NMD3B_RAT 413 560 DBREF 2RCA B 3 150 UNP Q8VHN2 NMD3B_RAT 413 560 DBREF 2RCA A 153 292 UNP Q8VHN2 NMD3B_RAT 676 815 DBREF 2RCA B 153 292 UNP Q8VHN2 NMD3B_RAT 676 815 SEQADV 2RCA GLY A 1 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCA SER A 2 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCA GLY A 151 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RCA THR A 152 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RCA GLY B 1 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCA SER B 2 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCA GLY A 151 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RCA THR A 152 UNP Q9R1M7 SEE REMARK 999 SEQRES 1 A 292 GLY SER ALA ARG PRO LYS LEU ARG VAL VAL THR LEU VAL SEQRES 2 A 292 GLU HIS PRO PHE VAL PHE THR ARG GLU SER ASP GLU ASP SEQRES 3 A 292 GLY GLN CYS PRO ALA GLY GLN LEU CYS LEU ASP PRO GLY SEQRES 4 A 292 THR ASN ASP SER ALA ARG LEU ASP ALA LEU PHE ALA ALA SEQRES 5 A 292 LEU VAL ASN GLY SER VAL PRO ARG THR LEU ARG ARG CYS SEQRES 6 A 292 CYS TYR GLY TYR CYS ILE ASP LEU LEU GLU ARG LEU ALA SEQRES 7 A 292 GLU ASP LEU ALA PHE ASP PHE GLU LEU TYR ILE VAL GLY SEQRES 8 A 292 ASP GLY LYS TYR GLY ALA LEU ARG ASP GLY ARG TRP THR SEQRES 9 A 292 GLY LEU VAL GLY ASP LEU LEU ALA GLY ARG ALA HIS MET SEQRES 10 A 292 ALA VAL THR SER PHE SER ILE ASN SER ALA ARG SER GLN SEQRES 11 A 292 VAL VAL ASP PHE THR SER PRO PHE PHE SER THR SER LEU SEQRES 12 A 292 GLY ILE MET VAL ARG THR ARG GLY THR GLU LEU SER GLY SEQRES 13 A 292 ILE HIS ASP PRO LYS LEU HIS HIS PRO SER GLN GLY PHE SEQRES 14 A 292 ARG PHE GLY THR VAL TRP GLU SER SER ALA GLU ALA TYR SEQRES 15 A 292 ILE LYS ALA SER PHE PRO GLU MET HIS ALA HIS MET ARG SEQRES 16 A 292 ARG HIS SER ALA PRO THR THR PRO HIS GLY VAL ALA MET SEQRES 17 A 292 LEU THR SER ASP PRO PRO LYS LEU ASN ALA PHE ILE MET SEQRES 18 A 292 ASP LYS SER LEU LEU ASP TYR GLU VAL SER ILE ASP ALA SEQRES 19 A 292 ASP CYS LYS LEU LEU THR VAL GLY LYS PRO PHE ALA ILE SEQRES 20 A 292 GLU GLY TYR GLY ILE GLY LEU PRO GLN ASN SER PRO LEU SEQRES 21 A 292 THR SER ASN LEU SER GLU PHE ILE SER ARG TYR LYS SER SEQRES 22 A 292 SER GLY PHE ILE ASP LEU LEU HIS ASP LYS TRP TYR LYS SEQRES 23 A 292 MET VAL PRO CYS GLY LYS SEQRES 1 B 292 GLY SER ALA ARG PRO LYS LEU ARG VAL VAL THR LEU VAL SEQRES 2 B 292 GLU HIS PRO PHE VAL PHE THR ARG GLU SER ASP GLU ASP SEQRES 3 B 292 GLY GLN CYS PRO ALA GLY GLN LEU CYS LEU ASP PRO GLY SEQRES 4 B 292 THR ASN ASP SER ALA ARG LEU ASP ALA LEU PHE ALA ALA SEQRES 5 B 292 LEU VAL ASN GLY SER VAL PRO ARG THR LEU ARG ARG CYS SEQRES 6 B 292 CYS TYR GLY TYR CYS ILE ASP LEU LEU GLU ARG LEU ALA SEQRES 7 B 292 GLU ASP LEU ALA PHE ASP PHE GLU LEU TYR ILE VAL GLY SEQRES 8 B 292 ASP GLY LYS TYR GLY ALA LEU ARG ASP GLY ARG TRP THR SEQRES 9 B 292 GLY LEU VAL GLY ASP LEU LEU ALA GLY ARG ALA HIS MET SEQRES 10 B 292 ALA VAL THR SER PHE SER ILE ASN SER ALA ARG SER GLN SEQRES 11 B 292 VAL VAL ASP PHE THR SER PRO PHE PHE SER THR SER LEU SEQRES 12 B 292 GLY ILE MET VAL ARG THR ARG GLY THR GLU LEU SER GLY SEQRES 13 B 292 ILE HIS ASP PRO LYS LEU HIS HIS PRO SER GLN GLY PHE SEQRES 14 B 292 ARG PHE GLY THR VAL TRP GLU SER SER ALA GLU ALA TYR SEQRES 15 B 292 ILE LYS ALA SER PHE PRO GLU MET HIS ALA HIS MET ARG SEQRES 16 B 292 ARG HIS SER ALA PRO THR THR PRO HIS GLY VAL ALA MET SEQRES 17 B 292 LEU THR SER ASP PRO PRO LYS LEU ASN ALA PHE ILE MET SEQRES 18 B 292 ASP LYS SER LEU LEU ASP TYR GLU VAL SER ILE ASP ALA SEQRES 19 B 292 ASP CYS LYS LEU LEU THR VAL GLY LYS PRO PHE ALA ILE SEQRES 20 B 292 GLU GLY TYR GLY ILE GLY LEU PRO GLN ASN SER PRO LEU SEQRES 21 B 292 THR SER ASN LEU SER GLU PHE ILE SER ARG TYR LYS SER SEQRES 22 B 292 SER GLY PHE ILE ASP LEU LEU HIS ASP LYS TRP TYR LYS SEQRES 23 B 292 MET VAL PRO CYS GLY LYS HET GLY A 901 5 HET GLY A 902 5 HET GOL A 903 6 HETNAM GLY GLYCINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GLY 2(C2 H5 N O2) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *527(H2 O) HELIX 1 1 ASP A 42 GLY A 56 1 15 HELIX 2 2 PRO A 59 THR A 61 5 3 HELIX 3 3 GLY A 68 ALA A 82 1 15 HELIX 4 4 THR A 104 ALA A 112 1 9 HELIX 5 5 ASN A 125 GLN A 130 1 6 HELIX 6 6 ASP A 159 HIS A 164 1 6 HELIX 7 7 SER A 177 PHE A 187 1 11 HELIX 8 8 PHE A 187 ARG A 195 1 9 HELIX 9 9 THR A 201 SER A 211 1 11 HELIX 10 10 LYS A 223 ASP A 233 1 11 HELIX 11 11 LEU A 260 SER A 274 1 15 HELIX 12 12 GLY A 275 TYR A 285 1 11 HELIX 13 13 ASP B 42 VAL B 54 1 13 HELIX 14 14 PRO B 59 THR B 61 5 3 HELIX 15 15 GLY B 68 LEU B 81 1 14 HELIX 16 16 THR B 104 ALA B 112 1 9 HELIX 17 17 ASN B 125 GLN B 130 1 6 HELIX 18 18 ASP B 159 HIS B 164 1 6 HELIX 19 19 SER B 177 PHE B 187 1 11 HELIX 20 20 PHE B 187 ARG B 195 1 9 HELIX 21 21 THR B 201 SER B 211 1 11 HELIX 22 22 LYS B 223 ASP B 233 1 11 HELIX 23 23 LEU B 260 GLY B 275 1 16 HELIX 24 24 GLY B 275 TYR B 285 1 11 SHEET 1 A 6 PHE A 19 GLU A 22 0 SHEET 2 A 6 ARG A 63 TYR A 67 -1 O TYR A 67 N PHE A 19 SHEET 3 A 6 GLN A 33 LEU A 36 -1 N GLN A 33 O CYS A 66 SHEET 4 A 6 ASP A 84 ILE A 89 1 O ILE A 89 N LEU A 36 SHEET 5 A 6 LYS A 6 THR A 11 1 N VAL A 9 O GLU A 86 SHEET 6 A 6 MET A 117 ALA A 118 1 O MET A 117 N VAL A 10 SHEET 1 B 2 LEU A 98 ARG A 99 0 SHEET 2 B 2 ARG A 102 TRP A 103 -1 O ARG A 102 N ARG A 99 SHEET 1 C 2 VAL A 132 PHE A 134 0 SHEET 2 C 2 GLY A 253 PRO A 255 -1 O LEU A 254 N ASP A 133 SHEET 1 D 4 PHE A 171 GLY A 172 0 SHEET 2 D 4 ALA A 218 ASP A 222 1 O ILE A 220 N GLY A 172 SHEET 3 D 4 PHE A 139 ARG A 148 -1 N MET A 146 O PHE A 219 SHEET 4 D 4 LEU A 238 TYR A 250 -1 O PHE A 245 N LEU A 143 SHEET 1 E 6 PHE B 19 ARG B 21 0 SHEET 2 E 6 ARG B 63 TYR B 67 -1 O TYR B 67 N PHE B 19 SHEET 3 E 6 GLN B 33 LEU B 36 -1 N GLN B 33 O CYS B 66 SHEET 4 E 6 ASP B 84 ILE B 89 1 O LEU B 87 N LEU B 36 SHEET 5 E 6 LYS B 6 THR B 11 1 N VAL B 9 O GLU B 86 SHEET 6 E 6 MET B 117 ALA B 118 1 O MET B 117 N VAL B 10 SHEET 1 F 2 LEU B 98 ARG B 99 0 SHEET 2 F 2 ARG B 102 TRP B 103 -1 O ARG B 102 N ARG B 99 SHEET 1 G 2 VAL B 132 PHE B 134 0 SHEET 2 G 2 GLY B 253 PRO B 255 -1 O LEU B 254 N ASP B 133 SHEET 1 H 4 PHE B 171 GLY B 172 0 SHEET 2 H 4 ALA B 218 ASP B 222 1 O ILE B 220 N GLY B 172 SHEET 3 H 4 PHE B 139 ARG B 148 -1 N MET B 146 O PHE B 219 SHEET 4 H 4 LEU B 238 TYR B 250 -1 O PHE B 245 N LEU B 143 SSBOND 1 CYS A 29 CYS A 65 1555 1555 2.08 SSBOND 2 CYS A 35 CYS A 66 1555 1555 2.10 SSBOND 3 CYS B 29 CYS B 65 1555 1555 2.05 SSBOND 4 CYS B 35 CYS B 66 1555 1555 2.09 CISPEP 1 HIS A 15 PRO A 16 0 0.45 CISPEP 2 ASP A 212 PRO A 213 0 -3.52 CISPEP 3 HIS B 15 PRO B 16 0 0.50 CISPEP 4 VAL B 54 ASN B 55 0 6.14 CISPEP 5 ASP B 212 PRO B 213 0 -4.34 SITE 1 AC1 7 TYR A 95 SER A 121 SER A 123 ARG A 128 SITE 2 AC1 7 SER A 177 SER A 178 ASP A 222 SITE 1 AC2 7 TYR B 95 SER B 121 SER B 123 ARG B 128 SITE 2 AC2 7 SER B 177 SER B 178 ASP B 222 SITE 1 AC3 4 GLY A 113 HIS A 116 HOH A1114 HOH A1181 CRYST1 45.915 83.597 145.153 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006889 0.00000