HEADER APOPTOSIS 14-DEC-00 1HQ8 TITLE CRYSTAL STRUCTURE OF THE MURINE NK CELL-ACTIVATING RECEPTOR TITLE 2 NKG2D AT 1.95 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: NKG2-D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HOMODIMER, CIS-PROLINE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR D.W.WOLAN,L.TEYTON,M.G.RUDOLPH,B.VILLMOW,S.BAUER,D.H.BUSCH, AUTHOR 2 I.A.WILSON REVDAT 2 24-FEB-09 1HQ8 1 VERSN REVDAT 1 07-MAR-01 1HQ8 0 JRNL AUTH D.W.WOLAN,L.TEYTON,M.G.RUDOLPH,B.VILLMOW,S.BAUER, JRNL AUTH 2 D.H.BUSCH,I.A.WILSON JRNL TITL CRYSTAL STRUCTURE OF THE MURINE NK CELL-ACTIVATING JRNL TITL 2 RECEPTOR NKG2D AT 1.95 A. JRNL REF NAT.IMMUNOL. V. 2 248 2001 JRNL REFN ISSN 1529-2908 JRNL PMID 11224525 JRNL DOI 10.1038/85311 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 6848118.870 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 13099 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) : 0.215 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1340 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1762 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 188 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : -6.16000 REMARK 3 B33 (A**2) : 6.07000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.74 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) : 1.470 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.130 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.840 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.650 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 43.44 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HQ8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-00. REMARK 100 THE RCSB ID CODE IS RCSB012511. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.77500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, NA-CIT., PEG400, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 24.93000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.79000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.79000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.93000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.59500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.93000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.59500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.79000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.59500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.93000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.79000 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 SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: -X, 1/2-Y, Z 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 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 42.59500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 ILE A 176 CG1 CG2 CD1 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 A 53 O HOH A 69 2.14 REMARK 500 O HOH A 39 O HOH A 50 2.15 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 SER A 155 114.84 -164.08 REMARK 500 SER A 167 -161.99 67.66 REMARK 500 ALA A 178 -93.73 -71.61 REMARK 500 PRO A 201 128.99 -25.64 REMARK 500 LYS A 202 -37.05 83.09 REMARK 500 SER A 210 169.63 74.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 1HQ8 A 110 232 UNP O54709 NKG2D_MOUSE 110 232 SEQRES 1 A 123 GLY TYR CYS GLY PRO CYS PRO ASN ASN TRP ILE CYS HIS SEQRES 2 A 123 ARG ASN ASN CYS TYR GLN PHE PHE ASN GLU GLU LYS THR SEQRES 3 A 123 TRP ASN GLN SER GLN ALA SER CYS LEU SER GLN ASN SER SEQRES 4 A 123 SER LEU LEU LYS ILE TYR SER LYS GLU GLU GLN ASP PHE SEQRES 5 A 123 LEU LYS LEU VAL LYS SER TYR HIS TRP MET GLY LEU VAL SEQRES 6 A 123 GLN ILE PRO ALA ASN GLY SER TRP GLN TRP GLU ASP GLY SEQRES 7 A 123 SER SER LEU SER TYR ASN GLN LEU THR LEU VAL GLU ILE SEQRES 8 A 123 PRO LYS GLY SER CYS ALA VAL TYR GLY SER SER PHE LYS SEQRES 9 A 123 ALA TYR THR GLU ASP CYS ALA ASN LEU ASN THR TYR ILE SEQRES 10 A 123 CYS MET LYS ARG ALA VAL FORMUL 2 HOH *77(H2 O) HELIX 1 1 THR A 135 SER A 145 1 11 HELIX 2 2 GLN A 159 VAL A 165 5 7 SHEET 1 A11 ILE A 120 HIS A 122 0 SHEET 2 A11 ASN A 125 LYS A 134 -1 N ASN A 125 O HIS A 122 SHEET 3 A11 ASN A 223 LYS A 229 -1 O ASN A 223 N LYS A 134 SHEET 4 A11 SER A 149 LEU A 150 -1 O SER A 149 N MET A 228 SHEET 5 A11 ASN A 223 LYS A 229 -1 N MET A 228 O SER A 149 SHEET 6 A11 HIS A 169 GLN A 175 1 N TRP A 170 O THR A 224 SHEET 7 A11 TRP A 182 TRP A 184 -1 N GLN A 183 O VAL A 174 SHEET 8 A11 HIS A 169 GLN A 175 -1 N VAL A 174 O GLN A 183 SHEET 9 A11 CYS A 205 TYR A 208 -1 O ALA A 206 N MET A 171 SHEET 10 A11 LYS A 213 GLU A 217 -1 O TYR A 215 N VAL A 207 SHEET 11 A11 THR A 196 VAL A 198 1 O THR A 196 N ALA A 214 SSBOND 1 CYS A 112 CYS A 121 1555 1555 2.02 SSBOND 2 CYS A 115 CYS A 126 1555 1555 2.03 SSBOND 3 CYS A 143 CYS A 227 1555 1555 2.03 SSBOND 4 CYS A 205 CYS A 219 1555 1555 2.03 CISPEP 1 GLY A 113 PRO A 114 0 -0.33 CRYST1 49.860 85.190 87.580 90.00 90.00 90.00 I 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 0.020056 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011418 0.00000