HEADER 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 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 6 30-AUG-23 2RCB 1 REMARK SEQADV
REVDAT 5 23-AUG-17 2RCB 1 SOURCE
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,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) : 1.62
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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1876 ; 1.745 ; 2.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1630 ; 2.473 ; 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 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 20-SEP-07.
REMARK 100 THE DEPOSITION ID IS D_1000044688.
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 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 GOL A 902 6
HET DSN B 902 7
HETNAM DSN D-SERINE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 DSN 2(C3 H7 N O3)
FORMUL 4 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
(ATOM LINES ARE NOT SHOWN.)
END
