10 20 30 40 50 60 70 80 2RCB - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 19-SEP-07 2RCB
TITLE CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WITH D- TITLE 2 SERINE AT 1.62 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 2RCB 1 VERSN REVDAT 3 24-FEB-09 2RCB 1 VERSN REVDAT 2 19-AUG-08 2RCB 1 JRNL REVDAT 1 05-AUG-08 2RCB 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. 1.62 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 65305 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 : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 5525 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4683 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 400 REMARK 3 BIN FREE R VALUE : 0.2510 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 : 20 REMARK 3 SOLVENT ATOMS : 475 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) : 18.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : 0.00000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.529 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): 4615 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6273 ; 1.544 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 4.907 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;30.148 ;22.574 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 744 ;11.714 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;16.604 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 683 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3561 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2161 ; 0.220 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3282 ; 0.318 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 751 ; 0.192 ; 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): 52 ; 0.322 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.163 ; 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): 2939 ; 1.404 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4642 ; 1.988 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1876 ; 1.745 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1630 ; 2.473 ; 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 57 REMARK 3 ORIGIN FOR THE GROUP (A): 41.1016 26.0392 11.4856 REMARK 3 T TENSOR REMARK 3 T11: .0079 T22: .0897 REMARK 3 T33: .0766 T12: .0329 REMARK 3 T13: .0220 T23: .0256 REMARK 3 L TENSOR REMARK 3 L11: 1.9487 L22: 1.0432 REMARK 3 L33: 2.0860 L12: .5998 REMARK 3 L13: -.0422 L23: -.2791 REMARK 3 S TENSOR REMARK 3 S11: .0687 S12: .2769 S13: .1934 REMARK 3 S21: -.0535 S22: .0571 S23: .2271 REMARK 3 S31: -.2563 S32: -.2692 S33: -.1259 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 58 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): 56.9795 22.7024 21.8742 REMARK 3 T TENSOR REMARK 3 T11: .0369 T22: .0740 REMARK 3 T33: .0652 T12: -.0528 REMARK 3 T13: .0280 T23: -.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.1327 L22: .7172 REMARK 3 L33: 1.4135 L12: .0106 REMARK 3 L13: -.0651 L23: -.3427 REMARK 3 S TENSOR REMARK 3 S11: .1273 S12: -.0489 S13: .0460 REMARK 3 S21: .0808 S22: -.1029 S23: -.0575 REMARK 3 S31: -.1456 S32: .1796 S33: -.0244 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 266 REMARK 3 ORIGIN FOR THE GROUP (A): 56.8340 17.5827 26.1783 REMARK 3 T TENSOR REMARK 3 T11: .0294 T22: .0946 REMARK 3 T33: .0579 T12: -.0568 REMARK 3 T13: .0076 T23: .0030 REMARK 3 L TENSOR REMARK 3 L11: .9461 L22: 2.0877 REMARK 3 L33: 1.3379 L12: -.1624 REMARK 3 L13: -.1647 L23: -.5937 REMARK 3 S TENSOR REMARK 3 S11: .1219 S12: -.1208 S13: -.0191 REMARK 3 S21: .0825 S22: -.0821 S23: -.0149 REMARK 3 S31: -.0646 S32: .1568 S33: -.0398 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 267 A 285 REMARK 3 ORIGIN FOR THE GROUP (A): 44.4627 32.1334 33.9531 REMARK 3 T TENSOR REMARK 3 T11: .0647 T22: .0399 REMARK 3 T33: .0422 T12: -.0010 REMARK 3 T13: .0744 T23: -.0483 REMARK 3 L TENSOR REMARK 3 L11: .9392 L22: 5.8138 REMARK 3 L33: 2.3027 L12: -1.0871 REMARK 3 L13: -.5608 L23: 2.4927 REMARK 3 S TENSOR REMARK 3 S11: -.0289 S12: -.2479 S13: .1421 REMARK 3 S21: .0992 S22: .0940 S23: -.2415 REMARK 3 S31: -.1737 S32: -.0639 S33: -.0650 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): 62.4872 -14.7268 22.0383 REMARK 3 T TENSOR REMARK 3 T11: .0900 T22: .0415 REMARK 3 T33: .0368 T12: .0696 REMARK 3 T13: -.0351 T23: .0476 REMARK 3 L TENSOR REMARK 3 L11: 1.1086 L22: 2.0481 REMARK 3 L33: 1.4761 L12: -.3585 REMARK 3 L13: .1671 L23: .2998 REMARK 3 S TENSOR REMARK 3 S11: -.0720 S12: -.1232 S13: -.0309 REMARK 3 S21: .3363 S22: .0318 S23: -.3541 REMARK 3 S31: .1160 S32: .2746 S33: .0402 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): 48.7869 -8.2270 6.0049 REMARK 3 T TENSOR REMARK 3 T11: .0960 T22: .0357 REMARK 3 T33: .0378 T12: .0073 REMARK 3 T13: -.0203 T23: .0032 REMARK 3 L TENSOR REMARK 3 L11: 1.0056 L22: 1.8786 REMARK 3 L33: .8289 L12: -.6134 REMARK 3 L13: -.0101 L23: -.5396 REMARK 3 S TENSOR REMARK 3 S11: .0082 S12: -.0146 S13: -.0583 REMARK 3 S21: -.2783 S22: -.0059 S23: .0717 REMARK 3 S31: .1784 S32: -.0122 S33: -.0023 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 216 REMARK 3 ORIGIN FOR THE GROUP (A): 48.9753 2.0569 5.6374 REMARK 3 T TENSOR REMARK 3 T11: .1143 T22: .0138 REMARK 3 T33: .0301 T12: .0334 REMARK 3 T13: -.0043 T23: .0137 REMARK 3 L TENSOR REMARK 3 L11: .9003 L22: 3.2941 REMARK 3 L33: .8716 L12: -.6231 REMARK 3 L13: -.0615 L23: .9589 REMARK 3 S TENSOR REMARK 3 S11: .1317 S12: .0622 S13: .0503 REMARK 3 S21: -.3957 S22: -.1176 S23: -.0814 REMARK 3 S31: .1013 S32: -.0474 S33: -.0141 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 217 B 285 REMARK 3 ORIGIN FOR THE GROUP (A): 45.9466 -16.0793 14.1737 REMARK 3 T TENSOR REMARK 3 T11: .0610 T22: .0405 REMARK 3 T33: .0573 T12: -.0021 REMARK 3 T13: .0131 T23: .0252 REMARK 3 L TENSOR REMARK 3 L11: 1.3139 L22: 2.4226 REMARK 3 L33: .8097 L12: -.9339 REMARK 3 L13: .1035 L23: -.4129 REMARK 3 S TENSOR REMARK 3 S11: -.1155 S12: -.2075 S13: -.2243 REMARK 3 S21: -.0096 S22: .1061 S23: .3581 REMARK 3 S31: .1782 S32: -.0848 S33: .0094 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 2RCB 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 RCSB044688.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-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 : 71657 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1PB7 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 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 22.88950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.47950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.76050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.47950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.88950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.76050 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 IN THE PRESENT STRUCTURE PACKING IS NOT BIOLOGICALLY 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 HOH B 990 O HOH B 1093 1.83 REMARK 500 O HOH A 1134 O HOH A 1179 1.90 REMARK 500 O ALA B 31 O HOH B 934 1.97 REMARK 500 O HOH A 1098 O HOH A 1173 2.06 REMARK 500 O HOH A 1072 O HOH A 1181 2.08 REMARK 500 O HOH B 1021 O HOH B 1070 2.12 REMARK 500 NH1 ARG B 76 OD2 ASP B 80 2.15 REMARK 500 OD2 ASP B 159 O HOH B 1007 2.17 REMARK 500 OD2 ASP A 227 O HOH A 1170 2.19 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 LEU A 81 CA - CB - CG ANGL. DEV. = 14.3 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 120 -165.14 -175.40 REMARK 500 ALA B 51 20.09 -77.76 REMARK 500 ALA B 52 -34.86 -132.23 REMARK 500 THR B 120 -162.74 -175.43 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 A 967 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH A1070 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A1126 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH A1163 DISTANCE = 6.42 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN B 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 902
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RCA RELATED DB: PDB REMARK 900 NR3B COMPLEX WITH GLYCINE 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: 1PB8 RELATED DB: PDB REMARK 900 NR1 COMPLEX WITH D-SERINE
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 2RCB A 3 150 UNP Q8VHN2 NMD3B_RAT 413 560 DBREF 2RCB B 3 150 UNP Q8VHN2 NMD3B_RAT 413 560 DBREF 2RCB A 153 292 UNP Q8VHN2 NMD3B_RAT 676 815 DBREF 2RCB B 153 292 UNP Q8VHN2 NMD3B_RAT 676 815
SEQADV 2RCB GLY A 1 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCB SER A 2 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCB GLY A 151 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RCB THR A 152 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RCB GLY B 1 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCB SER B 2 UNP Q8VHN2 EXPRESSION TAG SEQADV 2RCB GLY A 151 UNP Q9R1M7 SEE REMARK 999 SEQADV 2RCB 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 DSN A 901 7 HET DSN B 902 7 HET GOL A 902 6
HETNAM DSN D-SERINE HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 DSN 2(C3 H7 N O3) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *475(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 LEU A 81 1 14 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 SER B 274 1 15 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 2.05 SSBOND 2 CYS A 35 CYS A 66 1555 1555 2.10 SSBOND 3 CYS B 29 CYS B 65 1555 1555 2.03 SSBOND 4 CYS B 35 CYS B 66 1555 1555 2.09
CISPEP 1 HIS A 15 PRO A 16 0 -0.15 CISPEP 2 ASP A 212 PRO A 213 0 -2.43 CISPEP 3 HIS B 15 PRO B 16 0 -0.97 CISPEP 4 VAL B 54 ASN B 55 0 2.30 CISPEP 5 ASP B 212 PRO B 213 0 -4.10
SITE 1 AC1 10 TYR A 95 SER A 121 SER A 123 ARG A 128 SITE 2 AC1 10 SER A 177 SER A 178 ALA A 179 MET A 221 SITE 3 AC1 10 ASP A 222 TYR A 250 SITE 1 AC2 10 TYR B 95 SER B 121 SER B 123 ARG B 128 SITE 2 AC2 10 SER B 177 SER B 178 ALA B 179 MET B 221 SITE 3 AC2 10 ASP B 222 TYR B 250 SITE 1 AC3 3 GLY A 113 HIS A 116 HOH A1089
CRYST1 45.779 83.521 144.959 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 0.021844 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011973 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006899 0.00000