HEADER IMMUNE SYSTEM 19-JAN-06 2FRG TITLE STRUCTURE OF THE IMMUNOGLOBULIN-LIKE DOMAIN OF HUMAN TLT-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TREM-LIKE TRANSCRIPT-1; COMPND 3 CHAIN: P; COMPND 4 FRAGMENT: IMMUNOGLOBULIN-LIKE DOMAIN 20-125; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TLT-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS IMMUNOGLOBULIN-LIKE, BETA-SANDWICH, CELL SURFACE RECEPTOR, TRIGGERING KEYWDS 2 RECEPTOR, TREM-LIKE, PLATELET RECEPTOR, ITIM, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.L.GATTIS,J.LUBKOWSKI REVDAT 6 06-NOV-24 2FRG 1 REMARK REVDAT 5 30-AUG-23 2FRG 1 REMARK REVDAT 4 18-OCT-17 2FRG 1 REMARK REVDAT 3 24-FEB-09 2FRG 1 VERSN REVDAT 2 23-MAY-06 2FRG 1 JRNL REVDAT 1 14-MAR-06 2FRG 0 JRNL AUTH J.L.GATTIS,A.V.WASHINGTON,M.M.CHISHOLM,L.QUIGLEY,A.SZYK, JRNL AUTH 2 D.W.MCVICAR,J.LUBKOWSKI JRNL TITL THE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF TRIGGERING JRNL TITL 2 RECEPTOR EXPRESSED ON MYELOID CELLS LIKE TRANSCRIPT-1 AND JRNL TITL 3 EVIDENCE FOR A NATURALLY OCCURRING SOLUBLE FRAGMENT. JRNL REF J.BIOL.CHEM. V. 281 13396 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16505478 JRNL DOI 10.1074/JBC.M600489200 REMARK 2 REMARK 2 RESOLUTION. 1.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 29945 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 + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1547 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1851 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 806 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.07000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.046 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.042 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.156 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 823 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1119 ; 1.452 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 105 ; 7.104 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 35 ;29.030 ;23.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 137 ;13.118 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;19.156 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 126 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 628 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 360 ; 0.259 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 548 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.192 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 33 ; 0.176 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 539 ; 1.492 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 848 ; 2.110 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 311 ; 3.067 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 271 ; 4.236 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1853 ; 1.766 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 152 ; 6.914 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1582 ; 2.882 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2FRG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036222. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-05; 10-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; APS REMARK 200 BEAMLINE : NULL; 22-ID REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54; 1.13 REMARK 200 MONOCHROMATOR : NULL; DOUBLE-CRYSTAL SI(220) REMARK 200 SAGITTAL FOCUSED REMARK 200 OPTICS : MIRRORS; MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31487 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.190 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: HYBRID MODEL CONTAINING STRUCTURALLY CONSERVED REMARK 200 RESIDUES OF TREM-1 (1SMO CHAIN A), NKP44(1HKF), AND D1 DOMAIN OF REMARK 200 POLYMERIC IMMUNOGLOBULIN RECEPTOR (1XED CHAIN E). REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOTHER LIQUOR CONTAINED 15-19% W/W REMARK 280 PEG6000, 0.5M NA/K PHOSPHATE PH 5.6. PROTEIN SOLUTION CONTAINED REMARK 280 10MG/ML TLT-1 IN 20MM TRIS PH 8. PROTEIN AND MOTHER LIQUOR WERE REMARK 280 MIXED IN EQUAL PROPORTIONS AT 15 C, AND HANGING DROPS WERE REMARK 280 SUSPENDED OVER MOTHER LIQUOR., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 23.54750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.99050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.54750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.99050 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 300 REMARK: CURRENT BIOCHEMICAL AND CRYSTALLOGRAPHIC EVIDENCE SUGGEST REMARK 300 THAT THE BIOLOGICALLY ACTIVE FORM IS MONOMERIC. 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: P 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 P 232 LIES ON A SPECIAL POSITION. REMARK 375 HOH P 277 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CB GLN P 37 O HOH P 276 1.69 REMARK 500 CG GLN P 37 O HOH P 276 2.12 REMARK 500 NE2 GLN P 37 O HOH P 276 2.12 REMARK 500 CD GLN P 37 O HOH P 276 2.13 REMARK 500 O HOH P 199 O HOH P 256 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 2FRG P 20 125 UNP Q86YW5 TRML1_HUMAN 20 125 SEQRES 1 P 106 GLY SER LEU PRO GLU VAL LEU GLN ALA PRO VAL GLY SER SEQRES 2 P 106 SER ILE LEU VAL GLN CYS HIS TYR ARG LEU GLN ASP VAL SEQRES 3 P 106 LYS ALA GLN LYS VAL TRP CYS ARG PHE LEU PRO GLU GLY SEQRES 4 P 106 CYS GLN PRO LEU VAL SER SER ALA VAL ASP ARG ARG ALA SEQRES 5 P 106 PRO ALA GLY ARG ARG THR PHE LEU THR ASP LEU GLY GLY SEQRES 6 P 106 GLY LEU LEU GLN VAL GLU MET VAL THR LEU GLN GLU GLU SEQRES 7 P 106 ASP ALA GLY GLU TYR GLY CYS MET VAL ASP GLY ALA ARG SEQRES 8 P 106 GLY PRO GLN ILE LEU HIS ARG VAL SER LEU ASN ILE LEU SEQRES 9 P 106 PRO PRO FORMUL 2 HOH *152(H2 O) HELIX 1 1 ARG P 41 VAL P 45 5 5 HELIX 2 2 GLN P 95 ALA P 99 5 5 SHEET 1 A 5 GLU P 24 ALA P 28 0 SHEET 2 A 5 GLY P 111 ILE P 122 1 O SER P 119 N GLU P 24 SHEET 3 A 5 GLY P 100 GLY P 108 -1 N GLY P 100 O LEU P 120 SHEET 4 A 5 GLN P 48 LEU P 55 -1 N VAL P 50 O MET P 105 SHEET 5 A 5 GLY P 58 SER P 64 -1 O LEU P 62 N TRP P 51 SHEET 1 B 4 ILE P 34 HIS P 39 0 SHEET 2 B 4 LEU P 86 MET P 91 -1 O VAL P 89 N VAL P 36 SHEET 3 B 4 THR P 77 GLY P 83 -1 N THR P 80 O GLN P 88 SHEET 4 B 4 ARG P 70 ALA P 73 -1 N ALA P 73 O THR P 77 SSBOND 1 CYS P 38 CYS P 104 1555 1555 2.05 SSBOND 2 CYS P 52 CYS P 59 1555 1555 2.05 CRYST1 47.095 79.981 25.780 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 0.021234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038790 0.00000