HEADER IMMUNE SYSTEM 11-MAR-08 3CIG TITLE CRYSTAL STRUCTURE OF MOUSE TLR3 ECTODOMAIN CAVEAT 3CIG NAG F 1 HAS WRONG CHIRALITY AT ATOM C1 NAG G 1 HAS WRONG CAVEAT 2 3CIG CHIRALITY AT ATOM C1 NAG H 1 HAS WRONG CHIRALITY AT ATOM C1 CAVEAT 3 3CIG NAG A 6621 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MOUSE TLR3 ECTODOMAIN (UNP RESIDUES 28-704); COMPND 5 SYNONYM: CD283 ANTIGEN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TLR3; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI-5; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS LEUCINE-RICH REPEAT, INNATE IMMUNITY, TLR, LRR, GLYCOPROTEIN, IMMUNE KEYWDS 2 RESPONSE, INFLAMMATORY RESPONSE, MEMBRANE, RECEPTOR, TRANSMEMBRANE, KEYWDS 3 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,I.BOTOS,Y.WANG,J.N.LEONARD,J.SHILOACH,D.M.SEGAL,D.R.DAVIES REVDAT 5 30-AUG-23 3CIG 1 HETSYN REVDAT 4 29-JUL-20 3CIG 1 CAVEAT COMPND REMARK SEQADV REVDAT 4 2 1 HETNAM LINK SITE ATOM REVDAT 3 13-JUL-11 3CIG 1 VERSN REVDAT 2 24-FEB-09 3CIG 1 VERSN REVDAT 1 06-MAY-08 3CIG 0 JRNL AUTH L.LIU,I.BOTOS,Y.WANG,J.N.LEONARD,J.SHILOACH,D.M.SEGAL, JRNL AUTH 2 D.R.DAVIES JRNL TITL STRUCTURAL BASIS OF TOLL-LIKE RECEPTOR 3 SIGNALING WITH JRNL TITL 2 DOUBLE-STRANDED RNA. JRNL REF SCIENCE V. 320 379 2008 JRNL REFN ISSN 0036-8075 JRNL PMID 18420935 JRNL DOI 10.1126/SCIENCE.1155406 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 31801 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1693 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) : 2.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.73 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1900 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3670 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.4290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 327 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.13000 REMARK 3 B22 (A**2) : -5.22000 REMARK 3 B33 (A**2) : 4.09000 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): 0.541 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.318 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.264 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.948 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5796 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7902 ; 1.758 ; 2.036 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 661 ; 5.704 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;44.647 ;25.234 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 976 ;19.934 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;22.050 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 973 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4127 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2593 ; 0.301 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3903 ; 0.355 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 178 ; 0.184 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): 37 ; 0.329 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.457 ; 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): 3370 ; 2.027 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5382 ; 3.239 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2630 ; 4.952 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2520 ; 7.184 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 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 3CIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 70 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 SI220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33494 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1250 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.790 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2A0Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 6000, 5% DEXTRAN 5000, 1M REMARK 280 LITHIUM CHLORIDE, 0.1M CITRIC ACID, PH 4.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.34050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.00850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 92.63900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.34050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.00850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.63900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.34050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.00850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 92.63900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.34050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.00850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 92.63900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 LYS A 547 REMARK 465 ARG A 548 REMARK 465 ALA A 549 REMARK 465 ASN A 550 REMARK 465 PRO A 551 REMARK 465 GLY A 552 REMARK 465 GLY A 553 REMARK 465 PRO A 554 REMARK 465 ASP A 698 REMARK 465 SER A 699 REMARK 465 ALA A 700 REMARK 465 PRO A 701 REMARK 465 PHE A 702 REMARK 465 GLU A 703 REMARK 465 ASN A 704 REMARK 465 LEU A 705 REMARK 465 TYR A 706 REMARK 465 PHE A 707 REMARK 465 GLN A 708 REMARK 465 GLY A 709 REMARK 465 HIS A 710 REMARK 465 HIS A 711 REMARK 465 HIS A 712 REMARK 465 HIS A 713 REMARK 465 HIS A 714 REMARK 465 HIS A 715 REMARK 465 TRP A 716 REMARK 465 SER A 717 REMARK 465 HIS A 718 REMARK 465 PRO A 719 REMARK 465 GLN A 720 REMARK 465 PHE A 721 REMARK 465 GLU A 722 REMARK 465 LYS A 723 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 O6 NDG F 2 O4 MAN F 3 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 6718 O HOH A 6718 2655 1.90 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 31 -157.51 -79.27 REMARK 500 TYR A 32 109.65 -53.89 REMARK 500 ASN A 33 14.98 50.90 REMARK 500 SER A 38 -80.85 -76.10 REMARK 500 HIS A 39 64.14 -101.54 REMARK 500 LYS A 41 34.40 73.31 REMARK 500 PRO A 50 174.07 -50.17 REMARK 500 LEU A 56 91.80 -178.44 REMARK 500 ASN A 61 -133.70 -113.30 REMARK 500 GLN A 62 16.05 -143.97 REMARK 500 PRO A 68 10.94 -65.62 REMARK 500 PHE A 84 60.75 74.75 REMARK 500 ASN A 85 -155.90 -136.52 REMARK 500 ILE A 87 133.14 -35.18 REMARK 500 LEU A 98 78.52 -118.39 REMARK 500 ASN A 109 -158.57 -93.74 REMARK 500 SER A 112 -79.03 -87.09 REMARK 500 CYS A 122 107.10 -56.84 REMARK 500 MET A 131 -45.47 -25.02 REMARK 500 SER A 134 74.29 35.01 REMARK 500 SER A 140 -143.91 72.75 REMARK 500 GLN A 146 47.35 -78.73 REMARK 500 HIS A 156 52.71 30.93 REMARK 500 ASN A 157 -156.37 -116.85 REMARK 500 GLN A 169 -157.73 -125.16 REMARK 500 LEU A 170 38.85 35.00 REMARK 500 GLU A 171 -43.90 -28.86 REMARK 500 ASN A 181 -159.78 -115.37 REMARK 500 SER A 205 152.00 -48.55 REMARK 500 LEU A 228 52.96 -118.37 REMARK 500 GLN A 251 -43.27 -135.31 REMARK 500 ASN A 258 -166.01 -128.57 REMARK 500 GLN A 259 52.64 -107.31 REMARK 500 ASN A 275 51.72 -103.01 REMARK 500 LEU A 297 56.69 -110.88 REMARK 500 LYS A 335 -167.59 -74.85 REMARK 500 SER A 337 152.19 68.83 REMARK 500 SER A 339 -81.57 -101.39 REMARK 500 PHE A 349 -10.34 81.58 REMARK 500 SER A 350 -28.74 -39.16 REMARK 500 ASP A 364 61.78 60.97 REMARK 500 SER A 369 -171.18 -178.73 REMARK 500 SER A 372 -0.81 -52.75 REMARK 500 ASN A 373 24.12 -147.78 REMARK 500 LEU A 386 38.75 -141.26 REMARK 500 LEU A 393 -91.09 -106.02 REMARK 500 GLN A 394 -35.32 77.08 REMARK 500 ASN A 398 4.22 -57.94 REMARK 500 ASN A 424 109.66 -26.43 REMARK 500 LEU A 430 55.44 -90.14 REMARK 500 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CIY RELATED DB: PDB DBREF 3CIG A 27 703 UNP Q99MB1 TLR3_MOUSE 28 704 SEQADV 3CIG ASN A 704 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG LEU A 705 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG TYR A 706 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG PHE A 707 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG GLN A 708 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG GLY A 709 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 710 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 711 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 712 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 713 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 714 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 715 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG TRP A 716 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG SER A 717 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG HIS A 718 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG PRO A 719 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG GLN A 720 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG PHE A 721 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG GLU A 722 UNP Q99MB1 EXPRESSION TAG SEQADV 3CIG LYS A 723 UNP Q99MB1 EXPRESSION TAG SEQRES 1 A 697 GLN CYS THR VAL ARG TYR ASN VAL ALA ASP CYS SER HIS SEQRES 2 A 697 LEU LYS LEU THR HIS ILE PRO ASP ASP LEU PRO SER ASN SEQRES 3 A 697 ILE THR VAL LEU ASN LEU THR HIS ASN GLN LEU ARG ARG SEQRES 4 A 697 LEU PRO PRO THR ASN PHE THR ARG TYR SER GLN LEU ALA SEQRES 5 A 697 ILE LEU ASP ALA GLY PHE ASN SER ILE SER LYS LEU GLU SEQRES 6 A 697 PRO GLU LEU CYS GLN ILE LEU PRO LEU LEU LYS VAL LEU SEQRES 7 A 697 ASN LEU GLN HIS ASN GLU LEU SER GLN ILE SER ASP GLN SEQRES 8 A 697 THR PHE VAL PHE CYS THR ASN LEU THR GLU LEU ASP LEU SEQRES 9 A 697 MET SER ASN SER ILE HIS LYS ILE LYS SER ASN PRO PHE SEQRES 10 A 697 LYS ASN GLN LYS ASN LEU ILE LYS LEU ASP LEU SER HIS SEQRES 11 A 697 ASN GLY LEU SER SER THR LYS LEU GLY THR GLY VAL GLN SEQRES 12 A 697 LEU GLU ASN LEU GLN GLU LEU LEU LEU ALA LYS ASN LYS SEQRES 13 A 697 ILE LEU ALA LEU ARG SER GLU GLU LEU GLU PHE LEU GLY SEQRES 14 A 697 ASN SER SER LEU ARG LYS LEU ASP LEU SER SER ASN PRO SEQRES 15 A 697 LEU LYS GLU PHE SER PRO GLY CYS PHE GLN THR ILE GLY SEQRES 16 A 697 LYS LEU PHE ALA LEU LEU LEU ASN ASN ALA GLN LEU ASN SEQRES 17 A 697 PRO HIS LEU THR GLU LYS LEU CYS TRP GLU LEU SER ASN SEQRES 18 A 697 THR SER ILE GLN ASN LEU SER LEU ALA ASN ASN GLN LEU SEQRES 19 A 697 LEU ALA THR SER GLU SER THR PHE SER GLY LEU LYS TRP SEQRES 20 A 697 THR ASN LEU THR GLN LEU ASP LEU SER TYR ASN ASN LEU SEQRES 21 A 697 HIS ASP VAL GLY ASN GLY SER PHE SER TYR LEU PRO SER SEQRES 22 A 697 LEU ARG TYR LEU SER LEU GLU TYR ASN ASN ILE GLN ARG SEQRES 23 A 697 LEU SER PRO ARG SER PHE TYR GLY LEU SER ASN LEU ARG SEQRES 24 A 697 TYR LEU SER LEU LYS ARG ALA PHE THR LYS GLN SER VAL SEQRES 25 A 697 SER LEU ALA SER HIS PRO ASN ILE ASP ASP PHE SER PHE SEQRES 26 A 697 GLN TRP LEU LYS TYR LEU GLU TYR LEU ASN MET ASP ASP SEQRES 27 A 697 ASN ASN ILE PRO SER THR LYS SER ASN THR PHE THR GLY SEQRES 28 A 697 LEU VAL SER LEU LYS TYR LEU SER LEU SER LYS THR PHE SEQRES 29 A 697 THR SER LEU GLN THR LEU THR ASN GLU THR PHE VAL SER SEQRES 30 A 697 LEU ALA HIS SER PRO LEU LEU THR LEU ASN LEU THR LYS SEQRES 31 A 697 ASN HIS ILE SER LYS ILE ALA ASN GLY THR PHE SER TRP SEQRES 32 A 697 LEU GLY GLN LEU ARG ILE LEU ASP LEU GLY LEU ASN GLU SEQRES 33 A 697 ILE GLU GLN LYS LEU SER GLY GLN GLU TRP ARG GLY LEU SEQRES 34 A 697 ARG ASN ILE PHE GLU ILE TYR LEU SER TYR ASN LYS TYR SEQRES 35 A 697 LEU GLN LEU SER THR SER SER PHE ALA LEU VAL PRO SER SEQRES 36 A 697 LEU GLN ARG LEU MET LEU ARG ARG VAL ALA LEU LYS ASN SEQRES 37 A 697 VAL ASP ILE SER PRO SER PRO PHE ARG PRO LEU ARG ASN SEQRES 38 A 697 LEU THR ILE LEU ASP LEU SER ASN ASN ASN ILE ALA ASN SEQRES 39 A 697 ILE ASN GLU ASP LEU LEU GLU GLY LEU GLU ASN LEU GLU SEQRES 40 A 697 ILE LEU ASP PHE GLN HIS ASN ASN LEU ALA ARG LEU TRP SEQRES 41 A 697 LYS ARG ALA ASN PRO GLY GLY PRO VAL ASN PHE LEU LYS SEQRES 42 A 697 GLY LEU SER HIS LEU HIS ILE LEU ASN LEU GLU SER ASN SEQRES 43 A 697 GLY LEU ASP GLU ILE PRO VAL GLY VAL PHE LYS ASN LEU SEQRES 44 A 697 PHE GLU LEU LYS SER ILE ASN LEU GLY LEU ASN ASN LEU SEQRES 45 A 697 ASN LYS LEU GLU PRO PHE ILE PHE ASP ASP GLN THR SER SEQRES 46 A 697 LEU ARG SER LEU ASN LEU GLN LYS ASN LEU ILE THR SER SEQRES 47 A 697 VAL GLU LYS ASP VAL PHE GLY PRO PRO PHE GLN ASN LEU SEQRES 48 A 697 ASN SER LEU ASP MET ARG PHE ASN PRO PHE ASP CYS THR SEQRES 49 A 697 CYS GLU SER ILE SER TRP PHE VAL ASN TRP ILE ASN GLN SEQRES 50 A 697 THR HIS THR ASN ILE SER GLU LEU SER THR HIS TYR LEU SEQRES 51 A 697 CYS ASN THR PRO HIS HIS TYR TYR GLY PHE PRO LEU LYS SEQRES 52 A 697 LEU PHE ASP THR SER SER CYS LYS ASP SER ALA PRO PHE SEQRES 53 A 697 GLU ASN LEU TYR PHE GLN GLY HIS HIS HIS HIS HIS HIS SEQRES 54 A 697 TRP SER HIS PRO GLN PHE GLU LYS MODRES 3CIG ASN A 70 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 196 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 252 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 275 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 291 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 398 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 667 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 413 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 507 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 662 ASN GLYCOSYLATION SITE MODRES 3CIG ASN A 424 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NDG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET FUL C 3 10 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NDG E 2 14 HET NAG F 1 14 HET NDG F 2 14 HET MAN F 3 11 HET BMA F 4 11 HET MAN F 5 11 HET NAG G 1 14 HET NDG G 2 14 HET BMA G 3 11 HET FUL G 4 10 HET NAG H 1 14 HET NAG H 2 14 HET NAG A 724 14 HET NAG A1961 14 HET FUC A2916 11 HET NAG A6621 14 HET NAG A6671 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM FUL BETA-L-FUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE HETSYN FUL BETA-L-FUCOSE; 6-DEOXY-BETA-L-GALACTOPYRANOSE; L- HETSYN 2 FUL FUCOSE; FUCOSE; 6-DEOXY-BETA-L-GALACTOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 14(C8 H15 N O6) FORMUL 2 NDG 4(C8 H15 N O6) FORMUL 3 FUL 2(C6 H12 O5) FORMUL 6 MAN 2(C6 H12 O6) FORMUL 6 BMA 2(C6 H12 O6) FORMUL 11 FUC C6 H12 O5 FORMUL 14 HOH *79(H2 O) HELIX 1 1 PRO A 92 LEU A 98 1 7 HELIX 2 2 SER A 188 GLY A 195 5 8 HELIX 3 3 ASN A 234 SER A 246 1 13 HELIX 4 4 PHE A 268 LYS A 272 5 5 HELIX 5 5 PHE A 401 ALA A 405 5 5 HELIX 6 6 GLU A 626 GLN A 635 1 10 HELIX 7 7 THR A 650 THR A 664 1 15 HELIX 8 8 GLU A 670 TYR A 675 1 6 HELIX 9 9 PRO A 680 TYR A 684 5 5 HELIX 10 10 PRO A 687 PHE A 691 5 5 SHEET 1 A25 LEU A 56 ASN A 57 0 SHEET 2 A25 ILE A 79 ASP A 81 1 O ASP A 81 N LEU A 56 SHEET 3 A25 VAL A 103 ASN A 105 1 O ASN A 105 N LEU A 80 SHEET 4 A25 GLU A 127 ASP A 129 1 O GLU A 127 N LEU A 104 SHEET 5 A25 LYS A 151 ASP A 153 1 O LYS A 151 N LEU A 128 SHEET 6 A25 GLU A 175 LEU A 177 1 O LEU A 177 N LEU A 152 SHEET 7 A25 LYS A 201 ASP A 203 1 O ASP A 203 N LEU A 176 SHEET 8 A25 ALA A 225 LEU A 227 1 O LEU A 227 N LEU A 202 SHEET 9 A25 ASN A 252 SER A 254 1 O ASN A 252 N LEU A 226 SHEET 10 A25 GLN A 278 ASP A 280 1 O GLN A 278 N LEU A 253 SHEET 11 A25 TYR A 302 SER A 304 1 O SER A 304 N LEU A 279 SHEET 12 A25 TYR A 326 SER A 328 1 O TYR A 326 N LEU A 303 SHEET 13 A25 TYR A 359 ASN A 361 1 O ASN A 361 N LEU A 327 SHEET 14 A25 TYR A 383 SER A 385 1 O SER A 385 N LEU A 360 SHEET 15 A25 THR A 411 ASN A 413 1 O ASN A 413 N LEU A 384 SHEET 16 A25 ILE A 435 ASP A 437 1 O ASP A 437 N LEU A 412 SHEET 17 A25 GLU A 460 TYR A 462 1 O GLU A 460 N LEU A 436 SHEET 18 A25 ARG A 484 MET A 486 1 O ARG A 484 N ILE A 461 SHEET 19 A25 ILE A 510 ASP A 512 1 O ILE A 510 N LEU A 485 SHEET 20 A25 ILE A 534 ASP A 536 1 O ILE A 534 N LEU A 511 SHEET 21 A25 ILE A 566 ASN A 568 1 O ASN A 568 N LEU A 535 SHEET 22 A25 SER A 590 ASN A 592 1 O SER A 590 N LEU A 567 SHEET 23 A25 SER A 614 ASN A 616 1 O ASN A 616 N ILE A 591 SHEET 24 A25 SER A 639 ASP A 641 1 O ASP A 641 N LEU A 615 SHEET 25 A25 ASN A 667 ILE A 668 1 O ASN A 667 N LEU A 640 SHEET 1 B 2 ALA A 185 LEU A 186 0 SHEET 2 B 2 GLU A 211 PHE A 212 1 O GLU A 211 N LEU A 186 SHEET 1 C 2 SER A 198 LEU A 199 0 SHEET 2 C 2 LYS A 222 LEU A 223 1 O LYS A 222 N LEU A 199 SHEET 1 D 2 ALA A 262 THR A 263 0 SHEET 2 D 2 ASP A 288 VAL A 289 1 O ASP A 288 N THR A 263 SHEET 1 E 2 ARG A 312 LEU A 313 0 SHEET 2 E 2 ASN A 345 ILE A 346 1 O ASN A 345 N LEU A 313 SHEET 1 F 2 THR A 395 LEU A 396 0 SHEET 2 F 2 LYS A 421 ILE A 422 1 O LYS A 421 N LEU A 396 SHEET 1 G 3 GLU A 444 LYS A 446 0 SHEET 2 G 3 TYR A 468 GLN A 470 1 O GLN A 470 N GLN A 445 SHEET 3 G 3 LEU A 492 LYS A 493 1 O LYS A 493 N LEU A 469 SHEET 1 H 2 PHE A 647 ASP A 648 0 SHEET 2 H 2 CYS A 677 THR A 679 1 O ASN A 678 N PHE A 647 SSBOND 1 CYS A 28 CYS A 37 1555 1555 2.04 SSBOND 2 CYS A 95 CYS A 122 1555 1555 2.03 SSBOND 3 CYS A 649 CYS A 677 1555 1555 2.02 SSBOND 4 CYS A 651 CYS A 696 1555 1555 2.01 LINK ND2 ASN A 70 C1 NAG A 724 1555 1555 1.45 LINK ND2 ASN A 196 C1 NAG A1961 1555 1555 1.45 LINK ND2 ASN A 252 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 275 C1 NAG C 1 1555 1555 1.44 LINK ND2 ASN A 291 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 398 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 413 C1 NAG F 1 1555 1555 1.44 LINK ND2 ASN A 424 C1 NAG G 1 1555 1555 1.45 LINK ND2 ASN A 507 C1 NAG H 1 1555 1555 1.44 LINK ND2 ASN A 662 C1 NAG A6621 1555 1555 1.44 LINK ND2 ASN A 667 C1 NAG A6671 1555 1555 1.45 LINK O4 NAG B 1 C1 NDG B 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O6 NAG C 1 C1 FUL C 3 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG E 1 C1 NDG E 2 1555 1555 1.45 LINK O4 NAG F 1 C1 NDG F 2 1555 1555 1.45 LINK O4 NDG F 2 C1 MAN F 3 1555 1555 1.45 LINK O3 MAN F 3 C1 BMA F 4 1555 1555 1.45 LINK O6 MAN F 3 C1 MAN F 5 1555 1555 1.44 LINK O4 NAG G 1 C1 NDG G 2 1555 1555 1.45 LINK O6 NAG G 1 C1 FUL G 4 1555 1555 1.45 LINK O4 NDG G 2 C1 BMA G 3 1555 1555 1.45 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.45 CISPEP 1 SER A 498 PRO A 499 0 -4.70 CISPEP 2 THR A 679 PRO A 680 0 -8.14 CRYST1 82.681 158.017 185.278 90.00 90.00 90.00 I 2 2 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 0.012095 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005397 0.00000