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 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END