HEADER IMMUNE SYSTEM 02-DEC-08 3FF9 TITLE STRUCTURE OF NK CELL RECEPTOR KLRG1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY G MEMBER 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 75-188, C-TYPE LECTIN DOMAIN; COMPND 5 SYNONYM: MAST CELL FUNCTION-ASSOCIATED ANTIGEN 2F1, MAST CELL COMPND 6 FUNCTION-ASSOCIATED ANTIGEN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: KLRG1, MAFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI KEYWDS NATURAL KILLER CELL RECEPTOR KLTG1, GLYCOPROTEIN, LECTIN, MEMBRANE, KEYWDS 2 PHOSPHOPROTEIN, RECEPTOR, SIGNAL-ANCHOR, TRANSMEMBRANE, IMMUNE KEYWDS 3 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,R.A.MARIUZZA REVDAT 3 06-SEP-23 3FF9 1 SEQADV REVDAT 2 04-APR-18 3FF9 1 REMARK REVDAT 1 28-JUL-09 3FF9 0 JRNL AUTH Y.LI,M.HOFMANN,Q.WANG,L.TENG,L.K.CHLEWICKI,H.PIRCHER, JRNL AUTH 2 R.A.MARIUZZA JRNL TITL STRUCTURE OF NATURAL KILLER CELL RECEPTOR KLRG1 BOUND TO JRNL TITL 2 E-CADHERIN REVEALS BASIS FOR MHC-INDEPENDENT MISSING SELF JRNL TITL 3 RECOGNITION. JRNL REF IMMUNITY V. 31 35 2009 JRNL REFN ISSN 1074-7613 JRNL PMID 19604491 JRNL DOI 10.1016/J.IMMUNI.2009.04.019 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 20475 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 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 : 1861 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.89900 REMARK 3 B22 (A**2) : 2.99800 REMARK 3 B33 (A**2) : 1.90100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.45100 REMARK 3 B23 (A**2) : 0.00000 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 53.07 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3FF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.4SSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24208 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.230 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.98 REMARK 200 R MERGE FOR SHELL (I) : 0.34300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 1B6E AND 1E87 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA,KPO4, PH 8.0, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.56500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.46500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.56500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.46500 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, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: 3 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 8 LIES ON A SPECIAL POSITION. 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 TYR A 189 CG CD1 CD2 CE1 CE2 CZ OH 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 LEU A 78 -14.44 84.87 REMARK 500 ASN A 82 112.97 -164.12 REMARK 500 ASP A 139 49.94 -145.03 REMARK 500 LEU B 78 -15.06 86.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FF7 RELATED DB: PDB REMARK 900 RELATED ID: 3FF8 RELATED DB: PDB DBREF 3FF9 A 75 189 UNP O88713 KLRG1_MOUSE 75 188 DBREF 3FF9 B 75 189 UNP O88713 KLRG1_MOUSE 75 188 SEQADV 3FF9 MET A 74 UNP O88713 EXPRESSION TAG SEQADV 3FF9 MET B 74 UNP O88713 EXPRESSION TAG SEQRES 1 A 115 MET CYS PRO ILE LEU TRP THR ARG ASN GLY SER HIS CYS SEQRES 2 A 115 TYR TYR PHE SER MET GLU LYS LYS ASP TRP ASN SER SER SEQRES 3 A 115 LEU LYS PHE CYS ALA ASP LYS GLY SER HIS LEU LEU THR SEQRES 4 A 115 PHE PRO ASP ASN GLN GLY VAL LYS LEU PHE GLY GLU TYR SEQRES 5 A 115 LEU GLY GLN ASP PHE TYR TRP ILE GLY LEU ARG ASN ILE SEQRES 6 A 115 ASP GLY TRP ARG TRP GLU GLY GLY PRO ALA LEU SER LEU SEQRES 7 A 115 ARG ILE LEU THR ASN SER LEU ILE GLN ARG CYS GLY ALA SEQRES 8 A 115 ILE HIS ARG ASN GLY LEU GLN ALA SER SER CYS GLU VAL SEQRES 9 A 115 ALA LEU GLN TRP ILE CYS LYS LYS VAL LEU TYR SEQRES 1 B 115 MET CYS PRO ILE LEU TRP THR ARG ASN GLY SER HIS CYS SEQRES 2 B 115 TYR TYR PHE SER MET GLU LYS LYS ASP TRP ASN SER SER SEQRES 3 B 115 LEU LYS PHE CYS ALA ASP LYS GLY SER HIS LEU LEU THR SEQRES 4 B 115 PHE PRO ASP ASN GLN GLY VAL LYS LEU PHE GLY GLU TYR SEQRES 5 B 115 LEU GLY GLN ASP PHE TYR TRP ILE GLY LEU ARG ASN ILE SEQRES 6 B 115 ASP GLY TRP ARG TRP GLU GLY GLY PRO ALA LEU SER LEU SEQRES 7 B 115 ARG ILE LEU THR ASN SER LEU ILE GLN ARG CYS GLY ALA SEQRES 8 B 115 ILE HIS ARG ASN GLY LEU GLN ALA SER SER CYS GLU VAL SEQRES 9 B 115 ALA LEU GLN TRP ILE CYS LYS LYS VAL LEU TYR FORMUL 3 HOH *169(H2 O) HELIX 1 1 ASP A 95 LYS A 106 1 12 HELIX 2 2 GLY A 118 GLU A 124 1 7 HELIX 3 3 ASP B 95 LYS B 106 1 12 HELIX 4 4 GLY B 118 GLU B 124 1 7 SHEET 1 A 5 THR A 80 ASN A 82 0 SHEET 2 A 5 HIS A 85 PHE A 89 -1 O TYR A 87 N THR A 80 SHEET 3 A 5 GLN A 181 VAL A 187 -1 O LYS A 186 N CYS A 86 SHEET 4 A 5 TYR A 131 ASN A 137 1 N TRP A 132 O GLN A 181 SHEET 5 A 5 TRP A 141 TRP A 143 -1 O ARG A 142 N ARG A 136 SHEET 1 B 5 HIS A 109 LEU A 110 0 SHEET 2 B 5 GLN A 181 VAL A 187 -1 O LYS A 185 N HIS A 109 SHEET 3 B 5 TYR A 131 ASN A 137 1 N TRP A 132 O GLN A 181 SHEET 4 B 5 CYS A 163 HIS A 167 -1 O GLY A 164 N LEU A 135 SHEET 5 B 5 GLY A 170 SER A 174 -1 O SER A 174 N CYS A 163 SHEET 1 C 5 THR B 80 ASN B 82 0 SHEET 2 C 5 HIS B 85 PHE B 89 -1 O TYR B 87 N THR B 80 SHEET 3 C 5 GLN B 181 VAL B 187 -1 O LYS B 186 N CYS B 86 SHEET 4 C 5 TYR B 131 ASN B 137 1 N TRP B 132 O GLN B 181 SHEET 5 C 5 TRP B 141 TRP B 143 -1 O ARG B 142 N ARG B 136 SHEET 1 D 5 HIS B 109 LEU B 110 0 SHEET 2 D 5 GLN B 181 VAL B 187 -1 O LYS B 185 N HIS B 109 SHEET 3 D 5 TYR B 131 ASN B 137 1 N TRP B 132 O GLN B 181 SHEET 4 D 5 CYS B 163 HIS B 167 -1 O GLY B 164 N LEU B 135 SHEET 5 D 5 GLY B 170 SER B 174 -1 O SER B 174 N CYS B 163 SSBOND 1 CYS A 75 CYS A 86 1555 1555 2.03 SSBOND 2 CYS A 103 CYS A 184 1555 1555 2.04 SSBOND 3 CYS A 163 CYS A 176 1555 1555 2.03 SSBOND 4 CYS B 75 CYS B 86 1555 1555 2.03 SSBOND 5 CYS B 103 CYS B 184 1555 1555 2.04 SSBOND 6 CYS B 163 CYS B 176 1555 1555 2.03 CRYST1 59.130 56.930 68.090 90.00 97.20 90.00 C 1 2 1 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 0.016912 0.000000 0.002136 0.00000 SCALE2 0.000000 0.017565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014803 0.00000