10 20 30 40 50 60 70 80 2RCA - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 DIPEPTIDE 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 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,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 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) : 1.62 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1859 ; 1.828 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1615 ; 2.653 ; 3.000 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 21-SEP-07. REMARK 100 THE RCSB ID CODE IS RCSB044687.
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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1105 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A1158 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH A1182 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A1201 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH B 496 DISTANCE = 5.20 ANGSTROMS
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 4 GOL C3 H8 O3 FORMUL 5 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