HEADER IMMUNE SYSTEM 10-JUN-03 1UFU TITLE CRYSTAL STRUCTURE OF LIGAND BINDING DOMAIN OF IMMUNOGLOBULIN-LIKE TITLE 2 TRANSCRIPT 2 (ILT2; LIR-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN-LIKE TRANSCRIPT 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (DOMAIN1 AND 2); COMPND 5 SYNONYM: ILT2; COMPND 6 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGMT7 KEYWDS IMMUNOGLOBULIN-LIKE FOLDS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.SHIROISHI,K.AMANO,L.RASUBALA,K.TSUMOTO,I.KUMAGAI,D.KOHDA,K.MAENAKA REVDAT 4 16-OCT-24 1UFU 1 REMARK REVDAT 3 25-OCT-23 1UFU 1 REMARK REVDAT 2 24-FEB-09 1UFU 1 VERSN REVDAT 1 10-AUG-04 1UFU 0 JRNL AUTH M.SHIROISHI,K.AMANO,L.RASUBALA,K.TSUMOTO,I.KUMAGAI,D.KOHDA, JRNL AUTH 2 K.MAENAKA JRNL TITL KINETIC AND THERMODYNAMIC PROPERTIES OF THE INTERACTION JRNL TITL 2 BETWEEN IMMUNOGLOBULIN LIKE TRANSCRIPT (ILT) AND MHC CLASS I JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 87.5 REMARK 3 NUMBER OF REFLECTIONS : 3607 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) : 0.232 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 339 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 68 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1355 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.40 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) : 0.41 REMARK 3 ESD FROM SIGMAA (A) : 0.42 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) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.57 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 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 : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000005781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4406 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 0.34400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB ENTRY 1G0X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM FORMATE, 0.08M NA-ACETATE, REMARK 280 PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 18.11000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.11000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.20000 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: 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 GLY A 137 REMARK 465 GLU A 138 REMARK 465 ASP A 139 REMARK 465 GLU A 140 REMARK 465 HIS A 141 REMARK 465 PRO A 142 REMARK 465 GLN A 143 REMARK 465 GLN A 148 REMARK 465 PRO A 149 REMARK 465 HIS A 150 REMARK 465 ALA A 151 REMARK 465 ARG A 152 REMARK 465 GLY A 153 REMARK 465 GLY A 162 REMARK 465 PRO A 163 REMARK 465 SER A 165 REMARK 465 PRO A 166 REMARK 465 SER A 167 REMARK 465 ARG A 168 REMARK 465 ARG A 169 REMARK 465 VAL A 196 REMARK 465 LEU A 197 REMARK 465 GLY A 198 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 -85.63 -179.93 REMARK 500 GLN A 33 -36.77 -145.90 REMARK 500 LYS A 41 -29.10 47.41 REMARK 500 TYR A 99 -117.05 -131.38 REMARK 500 SER A 181 56.50 -158.71 REMARK 500 SER A 186 -162.11 -76.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G0X RELATED DB: PDB REMARK 900 THE STRUCTURE FROM THE DIFFERENT FORM OF CRYSTAL (P21212) OF THE REMARK 900 SAME PROTEIN. DBREF 1UFU 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 HELIX 1 1 ALA A 44 ILE A 50 5 7 HELIX 2 2 PRO A 51 LYS A 56 1 6 SHEET 1 A 3 THR A 7 GLU A 11 0 SHEET 2 A 3 VAL A 22 GLN A 27 -1 O ARG A 25 N TRP A 9 SHEET 3 A 3 GLN A 59 ILE A 62 -1 O ILE A 62 N VAL A 22 SHEET 1 B 4 VAL A 15 THR A 17 0 SHEET 2 B 4 LEU A 91 THR A 96 1 O VAL A 94 N ILE A 16 SHEET 3 B 4 GLY A 71 SER A 79 -1 N TYR A 73 O LEU A 91 SHEET 4 B 4 GLY A 83 ARG A 84 -1 O GLY A 83 N SER A 79 SHEET 1 C 4 TYR A 35 ARG A 39 0 SHEET 2 C 4 GLY A 71 SER A 79 -1 O TYR A 76 N ARG A 36 SHEET 3 C 4 LEU A 91 THR A 96 -1 O LEU A 91 N TYR A 73 SHEET 4 C 4 GLU A 184 TRP A 185 1 O TRP A 185 N VAL A 95 SHEET 1 D 3 THR A 103 GLN A 107 0 SHEET 2 D 3 VAL A 118 ASP A 123 -1 O THR A 119 N GLN A 107 SHEET 3 D 3 ARG A 156 VAL A 161 -1 O PHE A 159 N LEU A 120 SHEET 1 E 4 LEU A 145 ASN A 146 0 SHEET 2 E 4 PHE A 131 CYS A 134 -1 N LEU A 133 O LEU A 145 SHEET 3 E 4 TRP A 171 ALA A 176 -1 O ARG A 173 N CYS A 134 SHEET 4 E 4 LEU A 192 GLU A 193 -1 O LEU A 192 N TYR A 172 SSBOND 1 CYS A 26 CYS A 75 1555 1555 2.06 SSBOND 2 CYS A 122 CYS A 174 1555 1555 2.03 SSBOND 3 CYS A 134 CYS A 144 1555 1555 2.03 CISPEP 1 GLU A 11 PRO A 12 0 2.36 CISPEP 2 GLN A 107 PRO A 108 0 1.68 CRYST1 36.220 104.400 53.460 90.00 90.00 90.00 P 21 21 2 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 0.027609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018706 0.00000