PDB Short entry for 1UGN HEADER IMMUNE SYSTEM 17-JUN-03 1UGN TITLE CRYSTAL STRUCTURE OF LIR1.02, ONE OF THE ALLELES OF LIR1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (DOMAIN1 AND 2); COMPND 5 SYNONYM: LIR1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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,L.RASUBALA,K.KUROKI,K.AMANO,N.TSUCHIYA,K.TOKUNAGA, AUTHOR 2 D.KOHDA,K.MAENAKA REVDAT 5 25-OCT-23 1UGN 1 REMARK REVDAT 4 10-NOV-21 1UGN 1 SEQADV REVDAT 3 04-OCT-17 1UGN 1 REMARK REVDAT 2 24-FEB-09 1UGN 1 VERSN REVDAT 1 10-AUG-04 1UGN 0 JRNL AUTH K.KUROKI,N.TSUCHIYA,M.SHIROISHI,L.RASUBALA,Y.YAMASHITA, JRNL AUTH 2 K.MATSUTA,T.FUKAZAWA,M.KUSAOI,Y.MURAKAMI,M.TAKIGUCHI,T.JUJI, JRNL AUTH 3 H.HASHIMOTO,D.KOHDA,K.MAENAKA,K.TOKUNAGA JRNL TITL EXTENSIVE POLYMORPHISMS OF LILRB1 (ILT2, LIR1) AND THEIR JRNL TITL 2 ASSOCIATION WITH HLA-DRB1 SHARED EPITOPE NEGATIVE RHEUMATOID JRNL TITL 3 ARTHRITIS. JRNL REF HUM.MOL.GENET. V. 14 2469 2005 JRNL REFN ISSN 0964-6906 JRNL PMID 16014635 JRNL DOI 10.1093/HMG/DDI247 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 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) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 18080 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 922 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1464 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.60 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1UGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000005801. 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 : 8.5 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) : 0.984 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 : 18378 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 95.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.030 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 1UFU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS CHLORIDE, 0.7M POTASSIUM REMARK 280 SODIUM TARTRATE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 18.21850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.70700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.21850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.70700 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 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 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 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 LYS A 41 -44.44 70.17 REMARK 500 SER A 181 70.17 -151.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G0X RELATED DB: PDB REMARK 900 THE STRUCTURE OF LIR1.03 FROM THE DIFFERENT FORM OF CRYSTAL FROM REMARK 900 THIS CRYSTAL. REMARK 900 RELATED ID: 1UFU RELATED DB: PDB REMARK 900 THE STRUCTURE OF LIR1.03 FROM THE SAME FORM OF CRYSTAL AS THIS REMARK 900 CRYSTAL. DBREF 1UGN A 1 198 UNP Q8NHL6 LIRB1_HUMAN 24 221 SEQADV 1UGN THR A 70 UNP Q8NHL6 ALA 93 ENGINEERED MUTATION SEQRES 1 A 198 GLY HIS LEU PRO LYS PRO THR LEU TRP ALA GLU PRO GLY SEQRES 2 A 198 SER VAL ILE THR GLN GLY SER PRO VAL THR LEU ARG CYS SEQRES 3 A 198 GLN GLY GLY GLN GLU THR GLN GLU TYR ARG LEU TYR ARG SEQRES 4 A 198 GLU LYS LYS THR ALA PRO TRP ILE THR ARG ILE PRO GLN SEQRES 5 A 198 GLU LEU VAL LYS LYS GLY GLN PHE PRO ILE PRO SER ILE SEQRES 6 A 198 THR TRP GLU HIS THR GLY ARG TYR ARG CYS TYR TYR GLY SEQRES 7 A 198 SER ASP THR ALA GLY ARG SER GLU SER SER ASP PRO LEU SEQRES 8 A 198 GLU LEU VAL VAL THR GLY ALA TYR ILE LYS PRO THR LEU SEQRES 9 A 198 SER ALA GLN PRO SER PRO VAL VAL ASN SER GLY GLY ASN SEQRES 10 A 198 VAL THR LEU GLN CYS ASP SER GLN VAL ALA PHE ASP GLY SEQRES 11 A 198 PHE ILE LEU CYS LYS GLU GLY GLU ASP GLU HIS PRO GLN SEQRES 12 A 198 CYS LEU ASN SER GLN PRO HIS ALA ARG GLY SER SER ARG SEQRES 13 A 198 ALA ILE PHE SER VAL GLY PRO VAL SER PRO SER ARG ARG SEQRES 14 A 198 TRP TRP TYR ARG CYS TYR ALA TYR ASP SER ASN SER PRO SEQRES 15 A 198 TYR GLU TRP SER LEU PRO SER ASP LEU LEU GLU LEU LEU SEQRES 16 A 198 VAL LEU GLY FORMUL 2 HOH *175(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 THR A 70 5 5 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 GLN A 121 N SER A 105 SHEET 3 D 3 ARG A 156 VAL A 161 -1 O PHE A 159 N LEU A 120 SHEET 1 E 5 VAL A 111 ASN A 113 0 SHEET 2 E 5 LEU A 192 LEU A 197 1 O LEU A 197 N VAL A 112 SHEET 3 E 5 TRP A 170 TYR A 177 -1 N TYR A 172 O LEU A 192 SHEET 4 E 5 GLY A 130 GLU A 136 -1 N CYS A 134 O ARG A 173 SHEET 5 E 5 CYS A 144 ASN A 146 -1 O LEU A 145 N LEU A 133 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 0.14 CISPEP 2 GLN A 107 PRO A 108 0 0.10 CISPEP 3 GLY A 162 PRO A 163 0 0.02 CRYST1 36.437 103.414 53.022 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 0.027445 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018860 0.00000