PDB Short entry for 1G0X HEADER IMMUNE SYSTEM 09-OCT-00 1G0X TITLE CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF LIR-1 TITLE 2 (ILT2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: D1D2 LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: LEUKOCYTE INHIBITORY RECEPTOR-1; LEUKOCYTE COMPND 6 IMMUNOGLOBULIN-LIKE RECEPTOR, SUBFAMILY B (WITH TM AND COMPND 7 ITIM DOMAINS), MEMBER 1; LEUKOCYTE IMMUNOGLOBULIN-LIKE COMPND 8 RECEPTOR 1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23 KEYWDS IMMUNOGLOBULIN FOLD, 3-10 HELIX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.L.CHAPMAN,A.P.HEIKEMA,A.P.WEST JR.,P.J.BJORKMAN REVDAT 2 24-FEB-09 1G0X 1 VERSN REVDAT 1 17-JAN-01 1G0X 0 JRNL AUTH T.L.CHAPMAN,A.P.HEIKEMA,A.P.WEST JR.,P.J.BJORKMAN JRNL TITL CRYSTAL STRUCTURE AND LIGAND BINDING PROPERTIES OF JRNL TITL 2 THE D1D2 REGION OF THE INHIBITORY RECEPTOR LIR-1 JRNL TITL 3 (ILT2). JRNL REF IMMUNITY V. 13 727 2000 JRNL REFN ISSN 1074-7613 JRNL PMID 11114384 JRNL DOI 10.1016/S1074-7613(00)00071-6 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1902676.830 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18542 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) : 0.214 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 900 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1698 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 99 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 : 1512 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.28000 REMARK 3 B22 (A**2) : 1.28000 REMARK 3 B33 (A**2) : -2.57000 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) : 0.16 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.81 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) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.100 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.970 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 49.83 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.PA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARA 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 1G0X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-00. REMARK 100 THE RCSB ID CODE IS RCSB012095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 1.000 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 : 21555 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.29700 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: NULL 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 (%): 64.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTARATE, TRIS, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.86700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.12900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.12900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.43350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.12900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.12900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 97.30050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.12900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.12900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.43350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.12900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.12900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 97.30050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.86700 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: MONOMERIC 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 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 29 REMARK 465 GLN A 30 REMARK 465 GLU A 31 REMARK 465 ASP A 139 REMARK 465 GLU A 140 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 3 -65.73 -138.73 REMARK 500 GLN A 33 -25.64 -142.24 REMARK 500 LYS A 41 -34.89 71.49 REMARK 500 SER A 155 33.97 -140.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 409 DISTANCE = 5.53 ANGSTROMS DBREF 1G0X A 2 198 UNP Q8NHL6 LIRB1_HUMAN 25 221 SEQRES 1 A 197 HIS LEU PRO LYS PRO THR LEU TRP ALA GLU PRO GLY SER SEQRES 2 A 197 VAL ILE THR GLN GLY SER PRO VAL THR LEU ARG CYS GLN SEQRES 3 A 197 GLY GLY GLN GLU THR GLN GLU TYR ARG LEU TYR ARG GLU SEQRES 4 A 197 LYS LYS THR ALA PRO TRP ILE THR ARG ILE PRO GLN GLU SEQRES 5 A 197 LEU VAL LYS LYS GLY GLN PHE PRO ILE PRO SER ILE THR SEQRES 6 A 197 TRP GLU HIS ALA GLY ARG TYR ARG CYS TYR TYR GLY SER SEQRES 7 A 197 ASP THR ALA GLY ARG SER GLU SER SER ASP PRO LEU GLU SEQRES 8 A 197 LEU VAL VAL THR GLY ALA TYR ILE LYS PRO THR LEU SER SEQRES 9 A 197 ALA GLN PRO SER PRO VAL VAL ASN SER GLY GLY ASN VAL SEQRES 10 A 197 THR LEU GLN CYS ASP SER GLN VAL ALA PHE ASP GLY PHE SEQRES 11 A 197 ILE LEU CYS LYS GLU GLY GLU ASP GLU HIS PRO GLN CYS SEQRES 12 A 197 LEU ASN SER GLN PRO HIS ALA ARG GLY SER SER ARG ALA SEQRES 13 A 197 ILE PHE SER VAL GLY PRO VAL SER PRO SER ARG ARG TRP SEQRES 14 A 197 TRP TYR ARG CYS TYR ALA TYR ASP SER ASN SER PRO TYR SEQRES 15 A 197 GLU TRP SER LEU PRO SER ASP LEU LEU GLU LEU LEU VAL SEQRES 16 A 197 LEU GLY FORMUL 2 HOH *245(H2 O) HELIX 1 1 ALA A 44 ARG A 49 1 6 HELIX 2 2 PRO A 51 LYS A 56 1 6 HELIX 3 3 THR A 66 ALA A 70 5 5 HELIX 4 4 GLN A 148 HIS A 150 5 3 SHEET 1 A 3 THR A 7 GLU A 11 0 SHEET 2 A 3 VAL A 22 GLN A 27 -1 N THR A 23 O GLU A 11 SHEET 3 A 3 GLN A 59 ILE A 62 -1 N PHE A 60 O LEU A 24 SHEET 1 B 4 THR A 103 GLN A 107 0 SHEET 2 B 4 VAL A 118 ASP A 123 -1 O THR A 119 N GLN A 107 SHEET 3 B 4 ARG A 156 VAL A 161 -1 O ALA A 157 N CYS A 122 SHEET 4 B 4 ARG A 152 GLY A 153 -1 N GLY A 153 O ARG A 156 SHEET 1 C 2 VAL A 111 ASN A 113 0 SHEET 2 C 2 LEU A 195 LEU A 197 1 O LEU A 195 N VAL A 112 SHEET 1 D 4 GLN A 143 ASN A 146 0 SHEET 2 D 4 GLY A 130 LYS A 135 -1 O LEU A 133 N LEU A 145 SHEET 3 D 4 TRP A 171 TYR A 177 -1 O ARG A 173 N CYS A 134 SHEET 4 D 4 LEU A 192 GLU A 193 -1 N LEU A 192 O TYR A 172 SSBOND 1 CYS A 26 CYS A 75 1555 1555 2.04 SSBOND 2 CYS A 122 CYS A 174 1555 1555 2.04 SSBOND 3 CYS A 134 CYS A 144 1555 1555 2.04 CISPEP 1 GLU A 11 PRO A 12 0 0.45 CISPEP 2 GLN A 107 PRO A 108 0 0.04 CISPEP 3 GLY A 162 PRO A 163 0 0.09 CRYST1 68.258 68.258 129.734 90.00 90.00 90.00 P 41 21 2 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 0.014650 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007708 0.00000