PDB Short entry for 1B88 HEADER IMMUNE SYSTEM 09-FEB-99 1B88 TITLE V-ALPHA 2.6 MOUSE T CELL RECEPTOR (TCR) DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: T CELL RECEPTOR V-ALPHA DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: V-ALPHA DOMAIN; COMPND 5 SYNONYM: TCR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: BALB/C; SOURCE 6 CELL_LINE: B4.2.3 T CELL HYBRIDOMA; SOURCE 7 CELL: T LYMPHOCYTE; SOURCE 8 CELLULAR_LOCATION: PLASMA MEMBRANE; SOURCE 9 GENE: TCRAV2S6J38; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_CELLULAR_LOCATION: INCLUSION BODIES; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS T CELL RECEPTOR, MHC CLASS I, HUMAN IMMUNODEFICIENCY VIRUS, MOLECULAR KEYWDS 2 RECOGNITION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.PLAKSIN,S.CHACKO,J.NAVAZA,D.H.MARGULIES,E.A.PADLAN REVDAT 6 09-AUG-23 1B88 1 REMARK REVDAT 5 06-NOV-19 1B88 1 JRNL REVDAT 4 24-FEB-09 1B88 1 VERSN REVDAT 3 03-JUN-03 1B88 1 HEADER REVDAT REVDAT 2 24-JUN-99 1B88 1 JRNL REVDAT 1 16-FEB-99 1B88 0 JRNL AUTH D.PLAKSIN,S.CHACKO,J.NAVAZA,D.H.MARGULIES,E.A.PADLAN JRNL TITL THE X-RAY CRYSTAL STRUCTURE OF A VALPHA2.6JALPHA38 MOUSE T JRNL TITL 2 CELL RECEPTOR DOMAIN AT 2.5 A RESOLUTION: ALTERNATE MODES OF JRNL TITL 3 DIMERIZATION AND CRYSTAL PACKING. JRNL REF J.MOL.BIOL. V. 289 1153 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10373358 JRNL DOI 10.1006/JMBI.1999.2855 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.PLAKSIN,S.CHACKO,P.MCPHIE,A.BAX,E.A.PADLAN,D.H.MARGULIES REMARK 1 TITL A T CELL RECEPTOR V ALPHA DOMAIN EXPRESSED IN BACTERIA: DOES REMARK 1 TITL 2 IT DIMERIZE IN SOLUTION? REMARK 1 REF J.EXP.MED. V. 184 1251 1996 REMARK 1 REFN ISSN 0022-1007 REMARK 1 PMID 8879196 REMARK 1 DOI 10.1084/JEM.184.4.1251 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.8 REMARK 3 NUMBER OF REFLECTIONS : 12193 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) : 0.224 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 617 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1794 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.729 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.89 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.282 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.EAP REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH.EAP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13408 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 39.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1TCR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 26.99350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.20100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.09350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.20100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.99350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.09350 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 PRO A 40 C - N - CA ANGL. DEV. = 9.2 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 GLN A 3 -71.19 -45.64 REMARK 500 PRO A 40 -28.73 -23.13 REMARK 500 GLU A 42 -166.22 -104.06 REMARK 500 LYS A 71 35.31 73.65 REMARK 500 SER A 80 91.69 -38.26 REMARK 500 SER A 85 98.72 -62.54 REMARK 500 SER B 249 -166.85 -111.38 REMARK 500 ILE B 250 124.80 -179.30 REMARK 500 ARG B 261 18.93 59.95 REMARK 500 PRO B 282 -9.86 -54.64 REMARK 500 ASP B 284 6.31 -66.29 REMARK 500 SER B 295 149.13 -179.21 REMARK 500 ASN B 299 95.42 -44.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 1B88 A 1 114 GB 1518838 U63546 56 169 DBREF 1B88 B 201 314 GB 1518838 U63546 56 169 SEQRES 1 A 114 MET GLN GLN VAL ARG GLN SER PRO GLN SER LEU THR VAL SEQRES 2 A 114 TRP GLU GLY GLU THR ALA ILE LEU ASN CYS SER TYR GLU SEQRES 3 A 114 ASN SER ALA PHE ASP TYR PHE PRO TRP TYR GLN GLN PHE SEQRES 4 A 114 PRO GLY GLU GLY PRO ALA LEU LEU ILE SER ILE LEU SER SEQRES 5 A 114 VAL SER ASN LYS LYS GLU ASP GLY ARG PHE THR ILE PHE SEQRES 6 A 114 PHE ASN LYS ARG GLU LYS LYS LEU SER LEU HIS ILE ALA SEQRES 7 A 114 ASP SER GLN PRO GLY ASP SER ALA THR TYR PHE CYS ALA SEQRES 8 A 114 ALA SER ALA SER PHE GLY ASP ASN SER LYS LEU ILE TRP SEQRES 9 A 114 GLY LEU GLY THR SER LEU VAL VAL ASN PRO SEQRES 1 B 114 MET GLN GLN VAL ARG GLN SER PRO GLN SER LEU THR VAL SEQRES 2 B 114 TRP GLU GLY GLU THR ALA ILE LEU ASN CYS SER TYR GLU SEQRES 3 B 114 ASN SER ALA PHE ASP TYR PHE PRO TRP TYR GLN GLN PHE SEQRES 4 B 114 PRO GLY GLU GLY PRO ALA LEU LEU ILE SER ILE LEU SER SEQRES 5 B 114 VAL SER ASN LYS LYS GLU ASP GLY ARG PHE THR ILE PHE SEQRES 6 B 114 PHE ASN LYS ARG GLU LYS LYS LEU SER LEU HIS ILE ALA SEQRES 7 B 114 ASP SER GLN PRO GLY ASP SER ALA THR TYR PHE CYS ALA SEQRES 8 B 114 ALA SER ALA SER PHE GLY ASP ASN SER LYS LEU ILE TRP SEQRES 9 B 114 GLY LEU GLY THR SER LEU VAL VAL ASN PRO FORMUL 3 HOH *24(H2 O) HELIX 1 1 PRO A 82 ASP A 84 5 3 HELIX 2 2 PRO B 282 ASP B 284 5 3 SHEET 1 A 5 VAL A 4 SER A 7 0 SHEET 2 A 5 ALA A 19 TYR A 25 -1 N SER A 24 O ARG A 5 SHEET 3 A 5 LYS A 72 ILE A 77 -1 N ILE A 77 O ALA A 19 SHEET 4 A 5 PHE A 62 ASN A 67 -1 N ASN A 67 O LYS A 72 SHEET 5 A 5 LYS A 56 GLU A 58 -1 N LYS A 57 O ILE A 64 SHEET 1 B 3 THR A 87 CYS A 90 0 SHEET 2 B 3 TYR A 32 GLN A 38 -1 N GLN A 38 O THR A 87 SHEET 3 B 3 ALA A 45 LEU A 51 -1 N ILE A 50 O PHE A 33 SHEET 1 C 2 ALA A 91 SER A 93 0 SHEET 2 C 2 LEU A 102 TRP A 104 -1 N ILE A 103 O ALA A 92 SHEET 1 D 5 VAL B 204 SER B 207 0 SHEET 2 D 5 ALA B 219 TYR B 225 -1 N SER B 224 O ARG B 205 SHEET 3 D 5 LYS B 272 ILE B 277 -1 N ILE B 277 O ALA B 219 SHEET 4 D 5 PHE B 262 ASN B 267 -1 N ASN B 267 O LYS B 272 SHEET 5 D 5 LYS B 256 GLU B 258 -1 N LYS B 257 O ILE B 264 SHEET 1 E 2 THR B 212 TRP B 214 0 SHEET 2 E 2 VAL B 311 ASN B 313 1 N VAL B 311 O VAL B 213 SHEET 1 F 3 THR B 287 CYS B 290 0 SHEET 2 F 3 TRP B 235 GLN B 238 -1 N GLN B 238 O THR B 287 SHEET 3 F 3 ALA B 245 ILE B 248 -1 N ILE B 248 O TRP B 235 SSBOND 1 CYS A 23 CYS A 90 1555 1555 2.03 SSBOND 2 CYS B 223 CYS B 290 1555 1555 2.02 CISPEP 1 SER A 7 PRO A 8 0 -0.18 CISPEP 2 SER B 207 PRO B 208 0 -0.09 CRYST1 53.987 76.187 88.402 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 0.018523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011312 0.00000 MTRIX1 1 0.934100 0.352093 -0.059063 -11.33330 1 MTRIX2 1 0.354109 -0.934792 0.027753 68.82410 1 MTRIX3 1 -0.045440 -0.046838 -0.997868 53.37910 1