HEADER DNA BINDING PROTEIN/DNA 11-JAN-14 3WPE TITLE CRYSTAL STRUCTURE OF BOVINE TLR9 IN COMPLEX WITH AGONISTIC TITLE 2 DNA1668_12MER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, UNP RESIDUES 25-815; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3'); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: TLR9; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_CELL: SCHNEIDER 2(S2); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS LEUCINE RICH REPEAT, RECEPTOR, INNATE IMMUNITY, DNA BINDING, KEYWDS 2 GLYCOSYLATION, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR U.OHTO,H.TANJI,T.SHIMIZU REVDAT 2 06-MAY-15 3WPE 1 JRNL REVDAT 1 11-FEB-15 3WPE 0 JRNL AUTH U.OHTO,T.SHIBATA,H.TANJI,H.ISHIDA,E.KRAYUKHINA,S.UCHIYAMA, JRNL AUTH 2 K.MIYAKE,T.SHIMIZU JRNL TITL STRUCTURAL BASIS OF CPG AND INHIBITORY DNA RECOGNITION BY JRNL TITL 2 TOLL-LIKE RECEPTOR 9 JRNL REF NATURE V. 520 702 2015 JRNL REFN ISSN 0028-0836 JRNL PMID 25686612 JRNL DOI 10.1038/NATURE14138 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 32294 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1717 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) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2334 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5628 REMARK 3 NUCLEIC ACID ATOMS : 124 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.85000 REMARK 3 B22 (A**2) : -2.02000 REMARK 3 B33 (A**2) : -1.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.418 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.281 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.224 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.279 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5903 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5654 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8050 ; 1.166 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12954 ; 0.779 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 709 ; 6.291 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;37.454 ;23.398 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 963 ;16.087 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;16.168 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 924 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6558 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1414 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 29 A 792 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3606 -0.0333 16.4411 REMARK 3 T TENSOR REMARK 3 T11: 0.0350 T22: 0.0893 REMARK 3 T33: 0.1020 T12: -0.0030 REMARK 3 T13: -0.0555 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.0997 L22: 0.0616 REMARK 3 L33: 0.0604 L12: 0.0021 REMARK 3 L13: -0.0674 L23: 0.0286 REMARK 3 S TENSOR REMARK 3 S11: -0.0077 S12: 0.0050 S13: -0.0077 REMARK 3 S21: -0.0205 S22: 0.0017 S23: 0.0108 REMARK 3 S31: -0.0024 S32: -0.0018 S33: 0.0060 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 4 C 9 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2549 -18.3153 29.1743 REMARK 3 T TENSOR REMARK 3 T11: 0.2982 T22: 0.1405 REMARK 3 T33: 0.1170 T12: 0.0180 REMARK 3 T13: -0.0111 T23: 0.0453 REMARK 3 L TENSOR REMARK 3 L11: 2.1721 L22: 0.2705 REMARK 3 L33: 0.9675 L12: 0.0946 REMARK 3 L13: 1.3499 L23: 0.2375 REMARK 3 S TENSOR REMARK 3 S11: -0.1195 S12: 0.1908 S13: 0.1548 REMARK 3 S21: 0.2699 S22: 0.0174 S23: 0.0087 REMARK 3 S31: 0.0995 S32: 0.0890 S33: 0.1020 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 3WPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB096625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 48.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3-5% PEG 4000, 0.2M NA ACETATE, 0.1M REMARK 280 NA CITRATE PH 5.5, 15% DMSO , VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 57.91000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.91000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 56.54000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 56480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -12.41541 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.27716 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 ARG A 21 REMARK 465 SER A 22 REMARK 465 PRO A 23 REMARK 465 TRP A 24 REMARK 465 GLU A 25 REMARK 465 GLY A 26 REMARK 465 THR A 27 REMARK 465 LEU A 28 REMARK 465 GLY A 428 REMARK 465 ALA A 429 REMARK 465 ALA A 430 REMARK 465 THR A 431 REMARK 465 PRO A 432 REMARK 465 ALA A 433 REMARK 465 ALA A 434 REMARK 465 ALA A 435 REMARK 465 LEU A 436 REMARK 465 GLY A 437 REMARK 465 GLU A 438 REMARK 465 VAL A 439 REMARK 465 ASP A 440 REMARK 465 SER A 441 REMARK 465 ARG A 442 REMARK 465 VAL A 443 REMARK 465 GLU A 444 REMARK 465 VAL A 445 REMARK 465 TRP A 446 REMARK 465 ARG A 447 REMARK 465 LEU A 448 REMARK 465 PRO A 449 REMARK 465 ARG A 450 REMARK 465 GLY A 451 REMARK 465 LEU A 452 REMARK 465 ALA A 453 REMARK 465 PRO A 454 REMARK 465 GLY A 455 REMARK 465 PRO A 456 REMARK 465 LEU A 457 REMARK 465 ASP A 458 REMARK 465 ALA A 459 REMARK 465 VAL A 460 REMARK 465 SER A 461 REMARK 465 SER A 462 REMARK 465 LYS A 463 REMARK 465 ASP A 464 REMARK 465 PHE A 465 REMARK 465 MET A 466 REMARK 465 PRO A 467 REMARK 465 SER A 745 REMARK 465 LEU A 746 REMARK 465 CYS A 764 REMARK 465 GLY A 765 REMARK 465 ALA A 766 REMARK 465 GLY A 781 REMARK 465 LEU A 782 REMARK 465 SER A 783 REMARK 465 ARG A 784 REMARK 465 ARG A 785 REMARK 465 GLN A 793 REMARK 465 LEU A 794 REMARK 465 GLN A 795 REMARK 465 GLY A 796 REMARK 465 ARG A 797 REMARK 465 SER A 798 REMARK 465 ILE A 799 REMARK 465 PHE A 800 REMARK 465 THR A 801 REMARK 465 GLN A 802 REMARK 465 ASP A 803 REMARK 465 LEU A 804 REMARK 465 ARG A 805 REMARK 465 LEU A 806 REMARK 465 CYS A 807 REMARK 465 LEU A 808 REMARK 465 ASP A 809 REMARK 465 GLU A 810 REMARK 465 THR A 811 REMARK 465 LEU A 812 REMARK 465 SER A 813 REMARK 465 LEU A 814 REMARK 465 ASP A 815 REMARK 465 GLU A 816 REMARK 465 PHE A 817 REMARK 465 LEU A 818 REMARK 465 VAL A 819 REMARK 465 PRO A 820 REMARK 465 ARG A 821 REMARK 465 DC C 1 REMARK 465 DA C 2 REMARK 465 DT C 3 REMARK 465 DC C 10 REMARK 465 DC C 11 REMARK 465 DT C 12 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 NH1 ARG A 73 O6 DG C 7 2.16 REMARK 500 O PRO A 390 OG SER A 415 2.18 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 PHE A 55 151.65 71.40 REMARK 500 CYS A 97 54.47 -154.35 REMARK 500 THR A 152 -169.29 -110.71 REMARK 500 MET A 173 66.85 -150.97 REMARK 500 CYS A 177 89.35 -152.33 REMARK 500 ARG A 185 -121.84 -121.04 REMARK 500 LEU A 205 58.89 -140.47 REMARK 500 ARG A 216 76.87 49.77 REMARK 500 ASN A 229 -141.25 -105.46 REMARK 500 HIS A 230 39.51 -142.30 REMARK 500 LEU A 239 40.29 -109.82 REMARK 500 LEU A 242 53.83 -104.44 REMARK 500 PRO A 276 -38.62 -38.72 REMARK 500 ASP A 301 -33.88 -36.56 REMARK 500 LEU A 306 68.75 -118.75 REMARK 500 ASN A 317 -157.82 -108.92 REMARK 500 LEU A 332 52.46 -116.52 REMARK 500 SER A 361 49.87 -174.57 REMARK 500 PHE A 374 93.02 72.34 REMARK 500 ASN A 424 -167.06 -115.51 REMARK 500 LEU A 471 7.90 83.73 REMARK 500 ARG A 492 2.07 85.50 REMARK 500 ASN A 504 -159.77 -102.28 REMARK 500 SER A 595 136.36 -174.56 REMARK 500 SER A 607 63.28 -119.38 REMARK 500 ASN A 685 -158.36 -84.02 REMARK 500 SER A 691 -154.52 -156.12 REMARK 500 VAL A 720 -70.55 3.95 REMARK 500 ASN A 733 -158.30 -121.67 REMARK 500 PRO A 759 67.95 -63.36 REMARK 500 ARG A 775 41.13 -105.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 469 ASN A 470 146.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 362 24.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WPB RELATED DB: PDB REMARK 900 RELATED ID: 3WPC RELATED DB: PDB REMARK 900 RELATED ID: 3WPD RELATED DB: PDB REMARK 900 RELATED ID: 3WPF RELATED DB: PDB REMARK 900 RELATED ID: 3WPG RELATED DB: PDB REMARK 900 RELATED ID: 3WPH RELATED DB: PDB REMARK 900 RELATED ID: 3WPI RELATED DB: PDB DBREF 3WPE A 25 815 UNP Q5I2M5 TLR9_BOVIN 25 815 DBREF 3WPE C 1 12 PDB 3WPE 3WPE 1 12 SEQADV 3WPE ARG A 21 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE SER A 22 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE PRO A 23 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE TRP A 24 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE GLU A 816 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE PHE A 817 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE LEU A 818 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE VAL A 819 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE PRO A 820 UNP Q5I2M5 EXPRESSION TAG SEQADV 3WPE ARG A 821 UNP Q5I2M5 EXPRESSION TAG SEQRES 1 A 801 ARG SER PRO TRP GLU GLY THR LEU PRO ALA PHE LEU PRO SEQRES 2 A 801 CYS GLU LEU GLN PRO HIS GLY GLN VAL ASP CYS ASN TRP SEQRES 3 A 801 LEU PHE LEU LYS SER VAL PRO HIS PHE SER ALA GLY ALA SEQRES 4 A 801 PRO ARG ALA ASN VAL THR SER LEU SER LEU ILE SER ASN SEQRES 5 A 801 ARG ILE HIS HIS LEU HIS ASP SER ASP PHE VAL HIS LEU SEQRES 6 A 801 SER ASN LEU ARG VAL LEU ASN LEU LYS TRP ASN CYS PRO SEQRES 7 A 801 PRO ALA GLY LEU SER PRO MET HIS PHE PRO CYS ARG MET SEQRES 8 A 801 THR ILE GLU PRO ASN THR PHE LEU ALA VAL PRO THR LEU SEQRES 9 A 801 GLU GLU LEU ASN LEU SER TYR ASN GLY ILE THR THR VAL SEQRES 10 A 801 PRO ALA LEU PRO SER SER LEU VAL SER LEU SER LEU SER SEQRES 11 A 801 HIS THR SER ILE LEU VAL LEU GLY PRO THR HIS PHE THR SEQRES 12 A 801 GLY LEU HIS ALA LEU ARG PHE LEU TYR MET ASP GLY ASN SEQRES 13 A 801 CYS TYR TYR MET ASN PRO CYS PRO ARG ALA LEU GLU VAL SEQRES 14 A 801 ALA PRO GLY ALA LEU LEU GLY LEU GLY ASN LEU THR HIS SEQRES 15 A 801 LEU SER LEU LYS TYR ASN ASN LEU THR GLU VAL PRO ARG SEQRES 16 A 801 ARG LEU PRO PRO SER LEU ASP THR LEU LEU LEU SER TYR SEQRES 17 A 801 ASN HIS ILE VAL THR LEU ALA PRO GLU ASP LEU ALA ASN SEQRES 18 A 801 LEU THR ALA LEU ARG VAL LEU ASP VAL GLY GLY ASN CYS SEQRES 19 A 801 ARG ARG CYS ASP HIS ALA ARG ASN PRO CYS ARG GLU CYS SEQRES 20 A 801 PRO LYS ASN PHE PRO LYS LEU HIS PRO ASP THR PHE SER SEQRES 21 A 801 HIS LEU SER ARG LEU GLU GLY LEU VAL LEU LYS ASP SER SEQRES 22 A 801 SER LEU TYR LYS LEU GLU LYS ASP TRP PHE ARG GLY LEU SEQRES 23 A 801 GLY ARG LEU GLN VAL LEU ASP LEU SER GLU ASN PHE LEU SEQRES 24 A 801 TYR ASP TYR ILE THR LYS THR THR ILE PHE ASN ASP LEU SEQRES 25 A 801 THR GLN LEU ARG ARG LEU ASN LEU SER PHE ASN TYR HIS SEQRES 26 A 801 LYS LYS VAL SER PHE ALA HIS LEU HIS LEU ALA SER SER SEQRES 27 A 801 PHE GLY SER LEU VAL SER LEU GLU LYS LEU ASP MET HIS SEQRES 28 A 801 GLY ILE PHE PHE ARG SER LEU THR ASN ILE THR LEU GLN SEQRES 29 A 801 SER LEU THR ARG LEU PRO LYS LEU GLN SER LEU HIS LEU SEQRES 30 A 801 GLN LEU ASN PHE ILE ASN GLN ALA GLN LEU SER ILE PHE SEQRES 31 A 801 GLY ALA PHE PRO SER LEU LEU PHE VAL ASP LEU SER ASP SEQRES 32 A 801 ASN ARG ILE SER GLY ALA ALA THR PRO ALA ALA ALA LEU SEQRES 33 A 801 GLY GLU VAL ASP SER ARG VAL GLU VAL TRP ARG LEU PRO SEQRES 34 A 801 ARG GLY LEU ALA PRO GLY PRO LEU ASP ALA VAL SER SER SEQRES 35 A 801 LYS ASP PHE MET PRO SER CYS ASN LEU ASN PHE THR LEU SEQRES 36 A 801 ASP LEU SER ARG ASN ASN LEU VAL THR ILE GLN GLN GLU SEQRES 37 A 801 MET PHE THR ARG LEU SER ARG LEU GLN CYS LEU ARG LEU SEQRES 38 A 801 SER HIS ASN SER ILE SER GLN ALA VAL ASN GLY SER GLN SEQRES 39 A 801 PHE VAL PRO LEU THR SER LEU ARG VAL LEU ASP LEU SER SEQRES 40 A 801 HIS ASN LYS LEU ASP LEU TYR HIS GLY ARG SER PHE THR SEQRES 41 A 801 GLU LEU PRO GLN LEU GLU ALA LEU ASP LEU SER TYR ASN SEQRES 42 A 801 SER GLN PRO PHE SER MET GLN GLY VAL GLY HIS ASN LEU SEQRES 43 A 801 SER PHE VAL ALA GLN LEU PRO SER LEU ARG TYR LEU SER SEQRES 44 A 801 LEU ALA HIS ASN GLY ILE HIS SER ARG VAL SER GLN LYS SEQRES 45 A 801 LEU SER SER ALA SER LEU ARG ALA LEU ASP PHE SER GLY SEQRES 46 A 801 ASN SER LEU SER GLN MET TRP ALA GLU GLY ASP LEU TYR SEQRES 47 A 801 LEU CYS PHE PHE LYS GLY LEU ARG ASN LEU VAL GLN LEU SEQRES 48 A 801 ASP LEU SER GLU ASN HIS LEU HIS THR LEU LEU PRO ARG SEQRES 49 A 801 HIS LEU ASP ASN LEU PRO LYS SER LEU ARG GLN LEU ARG SEQRES 50 A 801 LEU ARG ASP ASN ASN LEU ALA PHE PHE ASN TRP SER SER SEQRES 51 A 801 LEU THR VAL LEU PRO ARG LEU GLU ALA LEU ASP LEU ALA SEQRES 52 A 801 GLY ASN GLN LEU LYS ALA LEU SER ASN GLY SER LEU PRO SEQRES 53 A 801 PRO GLY ILE ARG LEU GLN LYS LEU ASP VAL SER SER ASN SEQRES 54 A 801 SER ILE GLY PHE VAL ILE PRO GLY PHE PHE VAL ARG ALA SEQRES 55 A 801 THR ARG LEU ILE GLU LEU ASN LEU SER ALA ASN ALA LEU SEQRES 56 A 801 LYS THR VAL ASP PRO SER TRP PHE GLY SER LEU ALA GLY SEQRES 57 A 801 THR LEU LYS ILE LEU ASP VAL SER ALA ASN PRO LEU HIS SEQRES 58 A 801 CYS ALA CYS GLY ALA ALA PHE VAL ASP PHE LEU LEU GLU SEQRES 59 A 801 ARG GLN GLU ALA VAL PRO GLY LEU SER ARG ARG VAL THR SEQRES 60 A 801 CYS GLY SER PRO GLY GLN LEU GLN GLY ARG SER ILE PHE SEQRES 61 A 801 THR GLN ASP LEU ARG LEU CYS LEU ASP GLU THR LEU SER SEQRES 62 A 801 LEU ASP GLU PHE LEU VAL PRO ARG SEQRES 1 C 12 DC DA DT DG DA DC DG DT DT DC DC DT FORMUL 3 HOH *31(H2 O) HELIX 1 1 PRO A 60 VAL A 64 5 5 HELIX 2 2 PRO A 159 THR A 163 5 5 HELIX 3 3 ALA A 235 ALA A 240 5 6 HELIX 4 4 HIS A 275 SER A 280 5 6 HELIX 5 5 GLU A 299 ARG A 304 1 6 HELIX 6 6 ASP A 321 THR A 326 1 6 HELIX 7 7 ALA A 356 SER A 361 5 6 HELIX 8 8 LEU A 383 LEU A 389 5 7 HELIX 9 9 LEU A 407 PHE A 413 5 7 HELIX 10 10 GLN A 486 THR A 491 5 6 HELIX 11 11 ASN A 553 SER A 558 1 6 HELIX 12 12 LEU A 566 LEU A 572 5 7 HELIX 13 13 SER A 607 TRP A 612 1 6 HELIX 14 14 LEU A 642 ASN A 648 1 7 HELIX 15 15 TRP A 668 LEU A 674 5 7 HELIX 16 16 ASP A 739 PHE A 743 5 5 HELIX 17 17 PHE A 768 ARG A 775 1 8 SHEET 1 A28 GLU A 35 LEU A 36 0 SHEET 2 A28 GLN A 41 ASP A 43 -1 O ASP A 43 N GLU A 35 SHEET 3 A28 SER A 66 SER A 68 1 O SER A 66 N VAL A 42 SHEET 4 A28 VAL A 90 ASN A 92 1 O ASN A 92 N LEU A 67 SHEET 5 A28 GLU A 126 ASN A 128 1 O GLU A 126 N LEU A 91 SHEET 6 A28 SER A 146 SER A 148 1 O SER A 146 N LEU A 127 SHEET 7 A28 PHE A 170 TYR A 172 1 O PHE A 170 N LEU A 147 SHEET 8 A28 HIS A 202 SER A 204 1 O HIS A 202 N LEU A 171 SHEET 9 A28 THR A 223 LEU A 225 1 O LEU A 225 N LEU A 203 SHEET 10 A28 VAL A 247 ASP A 249 1 O VAL A 247 N LEU A 224 SHEET 11 A28 GLY A 287 VAL A 289 1 O VAL A 289 N LEU A 248 SHEET 12 A28 VAL A 311 ASP A 313 1 O VAL A 311 N LEU A 288 SHEET 13 A28 ARG A 337 ASN A 339 1 O ASN A 339 N LEU A 312 SHEET 14 A28 LYS A 367 ASP A 369 1 O LYS A 367 N LEU A 338 SHEET 15 A28 SER A 394 HIS A 396 1 O HIS A 396 N LEU A 368 SHEET 16 A28 PHE A 418 ASP A 420 1 O PHE A 418 N LEU A 395 SHEET 17 A28 THR A 474 ASP A 476 1 O ASP A 476 N VAL A 419 SHEET 18 A28 CYS A 498 ARG A 500 1 O ARG A 500 N LEU A 475 SHEET 19 A28 VAL A 523 ASP A 525 1 O VAL A 523 N LEU A 499 SHEET 20 A28 ALA A 547 ASP A 549 1 O ASP A 549 N LEU A 524 SHEET 21 A28 TYR A 577 SER A 579 1 O TYR A 577 N LEU A 548 SHEET 22 A28 ALA A 600 ASP A 602 1 O ASP A 602 N LEU A 578 SHEET 23 A28 GLN A 630 ASP A 632 1 O ASP A 632 N LEU A 601 SHEET 24 A28 GLN A 655 ARG A 657 1 O ARG A 657 N LEU A 631 SHEET 25 A28 ALA A 679 ASP A 681 1 O ALA A 679 N LEU A 656 SHEET 26 A28 LYS A 703 ASP A 705 1 O LYS A 703 N LEU A 680 SHEET 27 A28 GLU A 727 ASN A 729 1 O ASN A 729 N LEU A 704 SHEET 28 A28 ILE A 752 ASP A 754 1 O ILE A 752 N LEU A 728 SHEET 1 B 2 HIS A 76 LEU A 77 0 SHEET 2 B 2 THR A 112 ILE A 113 1 O THR A 112 N LEU A 77 SHEET 1 C 2 VAL A 156 LEU A 157 0 SHEET 2 C 2 GLU A 188 VAL A 189 1 O GLU A 188 N LEU A 157 SHEET 1 D 2 SER A 377 LEU A 378 0 SHEET 2 D 2 GLN A 404 ALA A 405 1 O GLN A 404 N LEU A 378 SHEET 1 E 2 ALA A 689 LEU A 690 0 SHEET 2 E 2 PHE A 713 VAL A 714 1 O PHE A 713 N LEU A 690 SHEET 1 F 2 LEU A 760 HIS A 761 0 SHEET 2 F 2 CYS A 788 SER A 790 1 O GLY A 789 N LEU A 760 SSBOND 1 CYS A 34 CYS A 44 1555 1555 2.03 SSBOND 2 CYS A 97 CYS A 109 1555 1555 2.02 SSBOND 3 CYS A 177 CYS A 183 1555 1555 2.05 SSBOND 4 CYS A 254 CYS A 267 1555 1555 2.01 SSBOND 5 CYS A 257 CYS A 264 1555 1555 2.05 SSBOND 6 CYS A 469 CYS A 498 1555 1555 2.96 SSBOND 7 CYS A 762 CYS A 788 1555 1555 2.04 CISPEP 1 LEU A 32 PRO A 33 0 7.02 CISPEP 2 PHE A 271 PRO A 272 0 7.47 CISPEP 3 SER A 361 LEU A 362 0 7.01 CISPEP 4 SER A 790 PRO A 791 0 -11.97 CRYST1 115.820 113.080 67.430 90.00 100.61 90.00 C 1 2 1 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 0.008634 0.000000 0.001617 0.00000 SCALE2 0.000000 0.008843 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015088 0.00000