HEADER IMMUNE SYSTEM 01-JUL-08 3DMM TITLE CRYSTAL STRUCTURE OF THE CD8 ALPHA BETA/H-2DD COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-D ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ALPHA-1,2,3 REGIONS: RESIDUES 26-299; COMPND 5 SYNONYM: H-2D(D); COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2 MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 21-119; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: SYNTHETIC PEPTIDE; COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN; COMPND 18 CHAIN: C; COMPND 19 FRAGMENT: IG-LIKE V-TYPE DOMAIN: RESIDUES 28-149; COMPND 20 SYNONYM: T-CELL SURFACE GLYCOPROTEIN LYT-2, CD8A ANTIGEN; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD8 BETA CHAIN; COMPND 24 CHAIN: D; COMPND 25 FRAGMENT: IG-LIKE V-TYPE DOMAIN: RESIDUES 22-141; COMPND 26 SYNONYM: T-CELL SURFACE GLYCOPROTEIN LYT-3, T-CELL MEMBRANE COMPND 27 GLYCOPROTEIN LY-3, LYMPHOCYTE ANTIGEN 3, CD8B ANTIGEN; COMPND 28 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 GENE: H2-D1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: B2M; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: SYNTHETIC PEPTIDE; SOURCE 20 MOL_ID: 4; SOURCE 21 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 22 ORGANISM_TAXID: 10090; SOURCE 23 GENE: CD8A, LYT-2, LYT2; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 28 MOL_ID: 5; SOURCE 29 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 30 ORGANISM_TAXID: 10090; SOURCE 31 GENE: CD8B, CD8B1, LY-3, LYT-3, LYT3; SOURCE 32 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 33 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 34 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 35 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS T CELL CO-RECEPTOR CD8AB MHC COMPLEX, GLYCOPROTEIN, IMMUNE RESPONSE, KEYWDS 2 MEMBRANE, MHC I, PHOSPHOPROTEIN, TRANSMEMBRANE, IMMUNOGLOBULIN KEYWDS 3 DOMAIN, SECRETED, ENVELOPE PROTEIN, ALTERNATIVE SPLICING, KEYWDS 4 POLYMORPHISM, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.WANG,K.NATARAJAN,D.H.MARGULIES REVDAT 4 30-AUG-23 3DMM 1 SEQADV REVDAT 3 25-OCT-17 3DMM 1 REMARK REVDAT 2 18-AUG-09 3DMM 1 JRNL REVDAT 1 14-JUL-09 3DMM 0 JRNL AUTH R.WANG,K.NATARAJAN,D.H.MARGULIES JRNL TITL STRUCTURAL BASIS OF THE CD8ALPHABETA/MHC CLASS I JRNL TITL 2 INTERACTION: FOCUSED RECOGNITION ORIENTS CD8BETA TO A T CELL JRNL TITL 3 PROXIMAL POSITION. JRNL REF J.IMMUNOL. V. 183 2554 2009 JRNL REFN ISSN 0022-1767 JRNL PMID 19625641 JRNL DOI 10.4049/JIMMUNOL.0901276 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 92554.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 21800 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 SET) : 0.248 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1277 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2541 REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5057 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.73100 REMARK 3 B22 (A**2) : 3.48700 REMARK 3 B33 (A**2) : -17.21800 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.46 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 2.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.330 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.990 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.480 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.660 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.200 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 63.66 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22842 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 ENTRIES 1QO3, 2ATP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3000, 0.05M HEPES PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 39.73400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.77200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.34700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.77200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.73400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.34700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE ASYMMETRIC UNIT IS THE BIOLOGICAL COMPLEX, CONSISTING REMARK 300 OF CHAINS A,B,P,C,D. 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 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P, C, D 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 MET A 1 REMARK 465 GLY C -4 REMARK 465 SER C -3 REMARK 465 GLY C -2 REMARK 465 GLU C -1 REMARK 465 ALA C 0 REMARK 465 LYS C 1 REMARK 465 PRO C 2 REMARK 465 GLN C 3 REMARK 465 VAL C 122 REMARK 465 ASN C 123 REMARK 465 SER C 124 REMARK 465 THR C 125 REMARK 465 THR C 126 REMARK 465 THR C 127 REMARK 465 LYS C 128 REMARK 465 PRO C 129 REMARK 465 VAL C 130 REMARK 465 LEU C 131 REMARK 465 ARG C 132 REMARK 465 THR C 133 REMARK 465 PRO C 134 REMARK 465 SER C 135 REMARK 465 PRO C 136 REMARK 465 VAL C 137 REMARK 465 HIS C 138 REMARK 465 PRO C 139 REMARK 465 THR C 140 REMARK 465 GLY C 141 REMARK 465 THR C 142 REMARK 465 SER C 143 REMARK 465 GLN C 144 REMARK 465 PRO C 145 REMARK 465 GLN C 146 REMARK 465 ARG C 147 REMARK 465 PRO C 148 REMARK 465 GLU C 149 REMARK 465 ASP C 150 REMARK 465 CYS C 151 REMARK 465 ARG C 152 REMARK 465 PRO C 153 REMARK 465 ARG C 154 REMARK 465 GLY C 155 REMARK 465 SER C 156 REMARK 465 VAL C 157 REMARK 465 LYS C 158 REMARK 465 GLY C 159 REMARK 465 THR C 160 REMARK 465 GLY C 161 REMARK 465 SER D -2 REMARK 465 SER D -1 REMARK 465 ALA D 0 REMARK 465 THR D 124 REMARK 465 LYS D 125 REMARK 465 LYS D 126 REMARK 465 THR D 127 REMARK 465 THR D 128 REMARK 465 LEU D 129 REMARK 465 LYS D 130 REMARK 465 MET D 131 REMARK 465 LYS D 132 REMARK 465 LYS D 133 REMARK 465 LYS D 134 REMARK 465 LYS D 135 REMARK 465 GLN D 136 REMARK 465 CYS D 137 REMARK 465 PRO D 138 REMARK 465 PHE D 139 REMARK 465 PRO D 140 REMARK 465 HIS D 141 REMARK 465 PRO D 142 REMARK 465 GLU D 143 REMARK 465 THR D 144 REMARK 465 GLN D 145 REMARK 465 LYS D 146 REMARK 465 GLY D 147 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO D 119 CG CD 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 ASP D 39 O LYS D 41 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 53 O THR D 120 4445 2.14 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 GLN B 2 N - CA - C ANGL. DEV. = 26.3 DEGREES REMARK 500 PRO B 47 N - CA - C ANGL. DEV. = 19.9 DEGREES REMARK 500 ALA C 16 CB - CA - C ANGL. DEV. = -10.8 DEGREES REMARK 500 SER C 31 CB - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 ASP C 80 CB - CA - C ANGL. DEV. = 18.2 DEGREES REMARK 500 ASP C 80 N - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 ASN C 82 CB - CA - C ANGL. DEV. = -26.9 DEGREES REMARK 500 ASN C 82 N - CA - C ANGL. DEV. = -32.8 DEGREES REMARK 500 ASN C 83 C - N - CA ANGL. DEV. = 44.4 DEGREES REMARK 500 SER D 24 CB - CA - C ANGL. DEV. = 48.3 DEGREES REMARK 500 SER D 24 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 ILE D 25 C - N - CA ANGL. DEV. = 38.3 DEGREES REMARK 500 PRO D 40 CB - CA - C ANGL. DEV. = 14.6 DEGREES REMARK 500 PRO D 40 N - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 LYS D 41 N - CA - C ANGL. DEV. = -41.6 DEGREES REMARK 500 ASP D 42 CB - CA - C ANGL. DEV. = 15.9 DEGREES REMARK 500 ASP D 42 N - CA - CB ANGL. DEV. = -19.5 DEGREES REMARK 500 ALA D 122 CB - CA - C ANGL. DEV. = -9.8 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 ARG A 14 68.40 -157.48 REMARK 500 GLN A 54 32.62 -89.55 REMARK 500 PRO A 57 -36.96 -35.04 REMARK 500 TYR A 123 -64.24 -120.71 REMARK 500 LYS A 131 -53.48 -138.38 REMARK 500 GLU A 223 107.10 66.29 REMARK 500 TRP A 274 -71.40 -52.68 REMARK 500 GLN B 2 41.63 77.32 REMARK 500 PRO B 15 44.59 -71.68 REMARK 500 GLN B 29 11.68 57.99 REMARK 500 HIS B 31 137.30 -173.47 REMARK 500 TRP B 60 -2.90 81.13 REMARK 500 ASP C 15 40.38 -108.16 REMARK 500 LEU C 18 138.46 -36.41 REMARK 500 VAL C 32 119.44 -33.04 REMARK 500 SER C 33 -166.01 -122.92 REMARK 500 GLN C 34 -41.30 -131.56 REMARK 500 SER C 44 6.63 -68.39 REMARK 500 SER C 59 -61.83 -143.65 REMARK 500 ASN C 70 164.22 -49.26 REMARK 500 SER C 71 -54.31 68.22 REMARK 500 LEU C 74 -7.42 -144.56 REMARK 500 ASP C 80 155.51 178.00 REMARK 500 THR C 81 66.19 37.17 REMARK 500 ASN C 82 143.73 -35.22 REMARK 500 ASN C 83 2.76 86.61 REMARK 500 GLU C 97 104.39 -58.70 REMARK 500 PHE C 101 148.50 178.19 REMARK 500 ASN C 107 70.71 63.45 REMARK 500 SER C 108 16.42 54.20 REMARK 500 SER C 114 172.20 -58.92 REMARK 500 SER D 24 -138.96 50.99 REMARK 500 ILE D 25 -13.86 -148.20 REMARK 500 LYS D 27 -163.68 -103.08 REMARK 500 THR D 29 -60.36 -139.48 REMARK 500 SER D 30 135.49 -172.54 REMARK 500 ARG D 37 97.62 -68.26 REMARK 500 PRO D 40 132.99 -39.89 REMARK 500 LYS D 41 177.01 116.76 REMARK 500 LEU D 48 -62.80 -108.41 REMARK 500 LYS D 65 -53.05 74.63 REMARK 500 ASN D 68 31.41 -98.43 REMARK 500 SER D 74 -6.59 -57.09 REMARK 500 ASN D 85 66.62 37.74 REMARK 500 ASP D 92 -174.52 -174.62 REMARK 500 THR D 120 -75.06 -94.00 REMARK 500 THR D 121 -156.41 -175.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER D 24 ILE D 25 131.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 3DMM A 2 275 UNP P01900 HA12_MOUSE 26 299 DBREF 3DMM B 1 99 UNP Q91XJ8 Q91XJ8_MOUSE 21 119 DBREF 3DMM P 1 10 PDB 3DMM 3DMM 1 10 DBREF 3DMM C -4 161 UNP P01731 CD8A_MOUSE 23 188 DBREF 3DMM D -2 147 UNP P10300 CD8B_MOUSE 19 168 SEQADV 3DMM MET A 1 UNP P01900 EXPRESSION TAG SEQADV 3DMM MET B 0 UNP Q91XJ8 EXPRESSION TAG SEQRES 1 A 275 MET SER HIS SER LEU ARG TYR PHE VAL THR ALA VAL SER SEQRES 2 A 275 ARG PRO GLY PHE GLY GLU PRO ARG TYR MET GLU VAL GLY SEQRES 3 A 275 TYR VAL ASP ASN THR GLU PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 275 ALA GLU ASN PRO ARG TYR GLU PRO ARG ALA ARG TRP ILE SEQRES 5 A 275 GLU GLN GLU GLY PRO GLU TYR TRP GLU ARG GLU THR ARG SEQRES 6 A 275 ARG ALA LYS GLY ASN GLU GLN SER PHE ARG VAL ASP LEU SEQRES 7 A 275 ARG THR ALA LEU ARG TYR TYR ASN GLN SER ALA GLY GLY SEQRES 8 A 275 SER HIS THR LEU GLN TRP MET ALA GLY CYS ASP VAL GLU SEQRES 9 A 275 SER ASP GLY ARG LEU LEU ARG GLY TYR TRP GLN PHE ALA SEQRES 10 A 275 TYR ASP GLY CYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 275 LYS THR TRP THR ALA ALA ASP MET ALA ALA GLN ILE THR SEQRES 12 A 275 ARG ARG LYS TRP GLU GLN ALA GLY ALA ALA GLU ARG ASP SEQRES 13 A 275 ARG ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU ARG SEQRES 14 A 275 ARG TYR LEU LYS ASN GLY ASN ALA THR LEU LEU ARG THR SEQRES 15 A 275 ASP PRO PRO LYS ALA HIS VAL THR HIS HIS ARG ARG PRO SEQRES 16 A 275 GLU GLY ASP VAL THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 275 TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN GLY SEQRES 18 A 275 GLU GLU LEU THR GLN GLU MET GLU LEU VAL GLU THR ARG SEQRES 19 A 275 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA SER VAL SEQRES 20 A 275 VAL VAL PRO LEU GLY LYS GLU GLN LYS TYR THR CYS HIS SEQRES 21 A 275 VAL GLU HIS GLU GLY LEU PRO GLU PRO LEU THR LEU ARG SEQRES 22 A 275 TRP GLY SEQRES 1 B 100 MET ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS SEQRES 3 B 100 TYR VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN SEQRES 4 B 100 MET LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SEQRES 5 B 100 SER ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE SEQRES 6 B 100 LEU ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR SEQRES 7 B 100 TYR ALA CYS ARG VAL LYS HIS ALA SER MET ALA GLU PRO SEQRES 8 B 100 LYS THR VAL TYR TRP ASP ARG ASP MET SEQRES 1 P 10 ARG GLY PRO GLY ARG ALA PHE VAL THR ILE SEQRES 1 C 166 GLY SER GLY GLU ALA LYS PRO GLN ALA PRO GLU LEU ARG SEQRES 2 C 166 ILE PHE PRO LYS LYS MET ASP ALA GLU LEU GLY GLN LYS SEQRES 3 C 166 VAL ASP LEU VAL CYS GLU VAL LEU GLY SER VAL SER GLN SEQRES 4 C 166 GLY CYS SER TRP LEU PHE GLN ASN SER SER SER LYS LEU SEQRES 5 C 166 PRO GLN PRO THR PHE VAL VAL TYR MET ALA SER SER HIS SEQRES 6 C 166 ASN LYS ILE THR TRP ASP GLU LYS LEU ASN SER SER LYS SEQRES 7 C 166 LEU PHE SER ALA MET ARG ASP THR ASN ASN LYS TYR VAL SEQRES 8 C 166 LEU THR LEU ASN LYS PHE SER LYS GLU ASN GLU GLY TYR SEQRES 9 C 166 TYR PHE CYS SER VAL ILE SER ASN SER VAL MET TYR PHE SEQRES 10 C 166 SER SER VAL VAL PRO VAL LEU GLN LYS VAL ASN SER THR SEQRES 11 C 166 THR THR LYS PRO VAL LEU ARG THR PRO SER PRO VAL HIS SEQRES 12 C 166 PRO THR GLY THR SER GLN PRO GLN ARG PRO GLU ASP CYS SEQRES 13 C 166 ARG PRO ARG GLY SER VAL LYS GLY THR GLY SEQRES 1 D 150 SER SER ALA LEU ILE GLN THR PRO SER SER LEU LEU VAL SEQRES 2 D 150 GLN THR ASN HIS THR ALA LYS MET SER CYS GLU VAL LYS SEQRES 3 D 150 SER ILE SER LYS LEU THR SER ILE TYR TRP LEU ARG GLU SEQRES 4 D 150 ARG GLN ASP PRO LYS ASP LYS TYR PHE GLU PHE LEU ALA SEQRES 5 D 150 SER TRP SER SER SER LYS GLY VAL LEU TYR GLY GLU SER SEQRES 6 D 150 VAL ASP LYS LYS ARG ASN ILE ILE LEU GLU SER SER ASP SEQRES 7 D 150 SER ARG ARG PRO PHE LEU SER ILE MET ASN VAL LYS PRO SEQRES 8 D 150 GLU ASP SER ASP PHE TYR PHE CYS ALA THR VAL GLY SER SEQRES 9 D 150 PRO LYS MET VAL PHE GLY THR GLY THR LYS LEU THR VAL SEQRES 10 D 150 VAL ASP VAL LEU PRO THR THR ALA PRO THR LYS LYS THR SEQRES 11 D 150 THR LEU LYS MET LYS LYS LYS LYS GLN CYS PRO PHE PRO SEQRES 12 D 150 HIS PRO GLU THR GLN LYS GLY FORMUL 6 HOH *37(H2 O) HELIX 1 1 TRP A 51 GLU A 55 5 5 HELIX 2 2 GLY A 56 TYR A 85 1 30 HELIX 3 3 ASP A 137 GLY A 151 1 15 HELIX 4 4 GLY A 151 GLY A 162 1 12 HELIX 5 5 GLY A 162 LEU A 180 1 19 HELIX 6 6 LYS A 253 GLN A 255 5 3 HELIX 7 7 GLU C 67 ASN C 70 5 4 HELIX 8 8 LYS D 87 SER D 91 5 5 SHEET 1 A 8 GLU A 46 PRO A 47 0 SHEET 2 A 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 A 8 ARG A 21 VAL A 28 -1 N VAL A 28 O THR A 31 SHEET 4 A 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 A 8 THR A 94 VAL A 103 -1 O VAL A 103 N HIS A 3 SHEET 6 A 8 LEU A 109 TYR A 118 -1 O TYR A 113 N GLY A 100 SHEET 7 A 8 CYS A 121 LEU A 126 -1 O ILE A 124 N PHE A 116 SHEET 8 A 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 B 4 LYS A 186 ARG A 193 0 SHEET 2 B 4 VAL A 199 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 B 4 PHE A 241 VAL A 249 -1 O ALA A 245 N CYS A 203 SHEET 4 B 4 GLU A 229 LEU A 230 -1 N GLU A 229 O SER A 246 SHEET 1 C 4 LYS A 186 ARG A 193 0 SHEET 2 C 4 VAL A 199 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 C 4 PHE A 241 VAL A 249 -1 O ALA A 245 N CYS A 203 SHEET 4 C 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 D 3 THR A 214 LEU A 219 0 SHEET 2 D 3 TYR A 257 GLU A 262 -1 O HIS A 260 N THR A 216 SHEET 3 D 3 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 E 4 GLN B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 E 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 E 4 GLU B 50 MET B 51 -1 N GLU B 50 O HIS B 67 SHEET 1 F 4 GLN B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 F 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 F 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 G 4 LYS B 44 LYS B 45 0 SHEET 2 G 4 GLU B 36 LYS B 41 -1 N LYS B 41 O LYS B 44 SHEET 3 G 4 TYR B 78 LYS B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 G 4 LYS B 91 TYR B 94 -1 O LYS B 91 N VAL B 82 SHEET 1 H 4 GLU C 6 PHE C 10 0 SHEET 2 H 4 VAL C 22 LEU C 29 -1 O GLU C 27 N ARG C 8 SHEET 3 H 4 LYS C 84 LEU C 89 -1 O LEU C 89 N VAL C 22 SHEET 4 H 4 PHE C 75 MET C 78 -1 N MET C 78 O VAL C 86 SHEET 1 I 5 ILE C 63 TRP C 65 0 SHEET 2 I 5 THR C 51 ALA C 57 -1 N TYR C 55 O THR C 64 SHEET 3 I 5 GLY C 35 ASN C 42 -1 N CYS C 36 O MET C 56 SHEET 4 I 5 GLY C 98 ILE C 105 -1 O PHE C 101 N LEU C 39 SHEET 5 I 5 MET C 110 PHE C 112 -1 O TYR C 111 N VAL C 104 SHEET 1 J 5 ILE C 63 TRP C 65 0 SHEET 2 J 5 THR C 51 ALA C 57 -1 N TYR C 55 O THR C 64 SHEET 3 J 5 GLY C 35 ASN C 42 -1 N CYS C 36 O MET C 56 SHEET 4 J 5 GLY C 98 ILE C 105 -1 O PHE C 101 N LEU C 39 SHEET 5 J 5 VAL C 116 VAL C 118 -1 O VAL C 116 N TYR C 100 SHEET 1 K 4 ILE D 2 THR D 4 0 SHEET 2 K 4 ALA D 16 GLU D 21 -1 O SER D 19 N THR D 4 SHEET 3 K 4 PHE D 80 ILE D 83 -1 O LEU D 81 N MET D 18 SHEET 4 K 4 ILE D 69 GLU D 72 -1 N GLU D 72 O PHE D 80 SHEET 1 L 6 SER D 7 GLN D 11 0 SHEET 2 L 6 THR D 110 VAL D 115 1 O LYS D 111 N LEU D 8 SHEET 3 L 6 ASP D 92 VAL D 99 -1 N TYR D 94 O THR D 110 SHEET 4 L 6 SER D 30 ARG D 37 -1 N GLU D 36 O PHE D 93 SHEET 5 L 6 TYR D 44 SER D 52 -1 O GLU D 46 N ARG D 35 SHEET 6 L 6 GLY D 56 TYR D 59 -1 O GLY D 56 N SER D 52 SHEET 1 M 4 SER D 7 GLN D 11 0 SHEET 2 M 4 THR D 110 VAL D 115 1 O LYS D 111 N LEU D 8 SHEET 3 M 4 ASP D 92 VAL D 99 -1 N TYR D 94 O THR D 110 SHEET 4 M 4 MET D 104 PHE D 106 -1 O VAL D 105 N THR D 98 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.05 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.03 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.04 SSBOND 4 CYS C 26 CYS C 102 1555 1555 2.04 SSBOND 5 CYS D 20 CYS D 96 1555 1555 2.02 CISPEP 1 TYR A 209 PRO A 210 0 0.25 CISPEP 2 HIS B 31 PRO B 32 0 0.20 CISPEP 3 PHE C 10 PRO C 11 0 0.12 CISPEP 4 THR D 4 PRO D 5 0 -0.22 CISPEP 5 SER D 101 PRO D 102 0 0.08 CRYST1 79.468 96.694 97.544 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010342 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010252 0.00000