HEADER DNA BINDING PROTEIN/DNA 11-JAN-14 3WPG TITLE CRYSTAL STRUCTURE OF MOUSE TLR9 IN COMPLEX WITH INHIBITORY DNA4084 TITLE 2 (FORM 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, UNP RESIDUES 26-818; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; 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, CPG MOTIF, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR U.OHTO,T.SHIMIZU REVDAT 3 29-JUL-20 3WPG 1 CAVEAT COMPND REMARK SEQADV REVDAT 3 2 1 HETNAM LINK SITE REVDAT 2 06-MAY-15 3WPG 1 JRNL REVDAT 1 11-FEB-15 3WPG 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. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 55710 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.6195 - 6.0869 0.99 2815 167 0.2344 0.2602 REMARK 3 2 6.0869 - 4.8352 1.00 2700 155 0.1978 0.2394 REMARK 3 3 4.8352 - 4.2251 1.00 2707 127 0.1769 0.1756 REMARK 3 4 4.2251 - 3.8393 1.00 2691 124 0.1823 0.2480 REMARK 3 5 3.8393 - 3.5644 1.00 2644 149 0.1880 0.2601 REMARK 3 6 3.5644 - 3.3544 1.00 2658 148 0.2184 0.2712 REMARK 3 7 3.3544 - 3.1865 1.00 2660 129 0.2436 0.2639 REMARK 3 8 3.1865 - 3.0479 1.00 2630 145 0.2544 0.3159 REMARK 3 9 3.0479 - 2.9306 1.00 2647 130 0.2712 0.3065 REMARK 3 10 2.9306 - 2.8295 1.00 2627 139 0.2742 0.3670 REMARK 3 11 2.8295 - 2.7411 1.00 2619 143 0.2656 0.3060 REMARK 3 12 2.7411 - 2.6628 1.00 2619 149 0.2761 0.2854 REMARK 3 13 2.6628 - 2.5927 1.00 2613 159 0.2785 0.3245 REMARK 3 14 2.5927 - 2.5295 1.00 2618 129 0.2892 0.3566 REMARK 3 15 2.5295 - 2.4720 1.00 2621 124 0.2994 0.3538 REMARK 3 16 2.4720 - 2.4194 1.00 2621 144 0.3197 0.3767 REMARK 3 17 2.4194 - 2.3710 1.00 2605 135 0.3406 0.4079 REMARK 3 18 2.3710 - 2.3263 1.00 2607 142 0.3602 0.4169 REMARK 3 19 2.3263 - 2.2847 1.00 2630 137 0.3755 0.3918 REMARK 3 20 2.2847 - 2.2460 0.99 2555 148 0.3928 0.4259 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.29 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 6206 REMARK 3 ANGLE : 0.888 8452 REMARK 3 CHIRALITY : 0.061 985 REMARK 3 PLANARITY : 0.003 1027 REMARK 3 DIHEDRAL : 16.302 2275 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -2.9957 4.8483 -25.3832 REMARK 3 T TENSOR REMARK 3 T11: 0.2644 T22: -0.0046 REMARK 3 T33: 0.2995 T12: -0.0414 REMARK 3 T13: 0.0341 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 1.6389 L22: 0.2309 REMARK 3 L33: 3.7257 L12: 0.0283 REMARK 3 L13: 0.9177 L23: 0.1224 REMARK 3 S TENSOR REMARK 3 S11: -0.0441 S12: 0.0916 S13: 0.0571 REMARK 3 S21: 0.0233 S22: 0.0593 S23: 0.0049 REMARK 3 S31: -0.1611 S32: -0.1384 S33: -0.0139 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000096627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A 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 : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.246 REMARK 200 RESOLUTION RANGE LOW (A) : 55.940 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) : NULL REMARK 200 R SYM (I) : 0.12000 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 (%): 59.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-8% PEG 8000, 0.4M AMMONIUM SULFATE, REMARK 280 0.1M TRIS PH 8.0, 10% DMSO , VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 35.61500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.93000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.61500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.93000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ARG A 22 REMARK 465 SER A 23 REMARK 465 PRO A 24 REMARK 465 TRP A 25 REMARK 465 LEU A 26 REMARK 465 GLY A 27 REMARK 465 PRO A 39 REMARK 465 HIS A 40 REMARK 465 SER A 57 REMARK 465 ALA A 58 REMARK 465 ALA A 59 REMARK 465 LEU A 103 REMARK 465 SER A 104 REMARK 465 PRO A 105 REMARK 465 LEU A 106 REMARK 465 HIS A 107 REMARK 465 PHE A 108 REMARK 465 LYS A 348 REMARK 465 VAL A 349 REMARK 465 SER A 350 REMARK 465 PHE A 351 REMARK 465 LEU A 433 REMARK 465 SER A 434 REMARK 465 GLU A 435 REMARK 465 ALA A 436 REMARK 465 THR A 437 REMARK 465 PRO A 438 REMARK 465 GLU A 439 REMARK 465 GLU A 440 REMARK 465 ALA A 441 REMARK 465 ASP A 442 REMARK 465 ASP A 443 REMARK 465 ALA A 444 REMARK 465 GLU A 445 REMARK 465 GLN A 446 REMARK 465 GLU A 447 REMARK 465 GLU A 448 REMARK 465 LEU A 449 REMARK 465 LEU A 450 REMARK 465 SER A 451 REMARK 465 ALA A 452 REMARK 465 ASP A 453 REMARK 465 PRO A 454 REMARK 465 HIS A 455 REMARK 465 PRO A 456 REMARK 465 ALA A 457 REMARK 465 PRO A 458 REMARK 465 LEU A 459 REMARK 465 SER A 460 REMARK 465 THR A 461 REMARK 465 PRO A 462 REMARK 465 ALA A 463 REMARK 465 SER A 464 REMARK 465 LYS A 465 REMARK 465 ASN A 466 REMARK 465 PHE A 467 REMARK 465 PRO A 559 REMARK 465 PHE A 560 REMARK 465 SER A 561 REMARK 465 MET A 562 REMARK 465 LYS A 563 REMARK 465 LEU A 811 REMARK 465 ASP A 812 REMARK 465 GLU A 813 REMARK 465 VAL A 814 REMARK 465 LEU A 815 REMARK 465 SER A 816 REMARK 465 TRP A 817 REMARK 465 ASP A 818 REMARK 465 GLU A 819 REMARK 465 PHE A 820 REMARK 465 LEU A 821 REMARK 465 VAL A 822 REMARK 465 PRO A 823 REMARK 465 ARG A 824 REMARK 465 DA B 12 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR A 28 CB OG1 CG2 REMARK 480 HIS A 281 C O CB CG ND1 CD2 CE1 REMARK 480 HIS A 281 NE2 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 ND2 ASN A 732 O5 NAG A 901 2.08 REMARK 500 OD1 ASN A 300 OG SER A 302 2.14 REMARK 500 OG1 THR A 325 O HIS A 355 2.16 REMARK 500 OD1 ASN A 129 OG SER A 131 2.16 REMARK 500 CB CYS A 767 SG CYS A 810 2.18 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 1024 O HOH A 1033 2555 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES 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 ASN A 73 -158.41 -90.20 REMARK 500 THR A 153 -165.53 -115.54 REMARK 500 CYS A 178 77.42 -151.95 REMARK 500 ASN A 230 -138.32 -111.62 REMARK 500 GLN A 242 -5.27 73.36 REMARK 500 LEU A 286 107.68 -59.77 REMARK 500 ASN A 318 -165.42 -116.36 REMARK 500 PHE A 319 70.79 -112.69 REMARK 500 LEU A 333 71.17 -69.14 REMARK 500 PHE A 375 69.29 61.96 REMARK 500 THR A 383 -44.18 -29.32 REMARK 500 ARG A 470 89.58 -163.07 REMARK 500 CYS A 471 -18.54 68.56 REMARK 500 ASN A 473 -26.26 62.10 REMARK 500 PHE A 476 100.85 -49.79 REMARK 500 ASN A 483 -150.55 -103.15 REMARK 500 ASN A 507 -162.02 -100.32 REMARK 500 ASN A 532 -166.41 -119.54 REMARK 500 ARG A 591 31.53 -90.18 REMARK 500 ASN A 609 -163.09 -111.87 REMARK 500 ASN A 664 -166.73 -103.89 REMARK 500 LEU A 690 94.08 -59.96 REMARK 500 LEU A 693 68.70 -115.78 REMARK 500 SER A 713 56.77 -111.07 REMARK 500 ASN A 736 -155.05 -105.73 REMARK 500 ALA A 769 126.36 -25.02 REMARK 500 ASN A 787 -30.54 -139.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1033 DISTANCE = 5.84 ANGSTROMS 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: 3WPE RELATED DB: PDB REMARK 900 RELATED ID: 3WPF RELATED DB: PDB REMARK 900 RELATED ID: 3WPH RELATED DB: PDB REMARK 900 RELATED ID: 3WPI RELATED DB: PDB DBREF 3WPG A 26 818 UNP Q9EQU3 TLR9_MOUSE 26 818 DBREF 3WPG B 1 12 PDB 3WPG 3WPG 1 12 SEQADV 3WPG ARG A 22 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG SER A 23 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG PRO A 24 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG TRP A 25 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG GLN A 200 UNP Q9EQU3 ASN 200 ENGINEERED MUTATION SEQADV 3WPG GLN A 242 UNP Q9EQU3 ASN 242 ENGINEERED MUTATION SEQADV 3WPG GLN A 309 UNP Q9EQU3 ASN 309 ENGINEERED MUTATION SEQADV 3WPG GLN A 495 UNP Q9EQU3 ASN 495 ENGINEERED MUTATION SEQADV 3WPG GLN A 568 UNP Q9EQU3 ASN 568 ENGINEERED MUTATION SEQADV 3WPG GLN A 695 UNP Q9EQU3 ASN 695 ENGINEERED MUTATION SEQADV 3WPG GLN A 752 UNP Q9EQU3 ASN 752 ENGINEERED MUTATION SEQADV 3WPG GLU A 819 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG PHE A 820 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG LEU A 821 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG VAL A 822 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG PRO A 823 UNP Q9EQU3 EXPRESSION TAG SEQADV 3WPG ARG A 824 UNP Q9EQU3 EXPRESSION TAG SEQRES 1 A 803 ARG SER PRO TRP LEU GLY THR LEU PRO ALA PHE LEU PRO SEQRES 2 A 803 CYS GLU LEU LYS PRO HIS GLY LEU VAL ASP CYS ASN TRP SEQRES 3 A 803 LEU PHE LEU LYS SER VAL PRO ARG PHE SER ALA ALA ALA SEQRES 4 A 803 SER CYS SER ASN ILE THR ARG LEU SER LEU ILE SER ASN SEQRES 5 A 803 ARG ILE HIS HIS LEU HIS ASN SER ASP PHE VAL HIS LEU SEQRES 6 A 803 SER ASN LEU ARG GLN LEU ASN LEU LYS TRP ASN CYS PRO SEQRES 7 A 803 PRO THR GLY LEU SER PRO LEU HIS PHE SER CYS HIS MET SEQRES 8 A 803 THR ILE GLU PRO ARG THR PHE LEU ALA MET ARG THR LEU SEQRES 9 A 803 GLU GLU LEU ASN LEU SER TYR ASN GLY ILE THR THR VAL SEQRES 10 A 803 PRO ARG LEU PRO SER SER LEU VAL ASN LEU SER LEU SER SEQRES 11 A 803 HIS THR ASN ILE LEU VAL LEU ASP ALA ASN SER LEU ALA SEQRES 12 A 803 GLY LEU TYR SER LEU ARG VAL LEU PHE MET ASP GLY ASN SEQRES 13 A 803 CYS TYR TYR LYS ASN PRO CYS THR GLY ALA VAL LYS VAL SEQRES 14 A 803 THR PRO GLY ALA LEU LEU GLY LEU SER GLN LEU THR HIS SEQRES 15 A 803 LEU SER LEU LYS TYR ASN ASN LEU THR LYS VAL PRO ARG SEQRES 16 A 803 GLN LEU PRO PRO SER LEU GLU TYR LEU LEU VAL SER TYR SEQRES 17 A 803 ASN LEU ILE VAL LYS LEU GLY PRO GLU ASP LEU ALA GLN SEQRES 18 A 803 LEU THR SER LEU ARG VAL LEU ASP VAL GLY GLY ASN CYS SEQRES 19 A 803 ARG ARG CYS ASP HIS ALA PRO ASN PRO CYS ILE GLU CYS SEQRES 20 A 803 GLY GLN LYS SER LEU HIS LEU HIS PRO GLU THR PHE HIS SEQRES 21 A 803 HIS LEU SER HIS LEU GLU GLY LEU VAL LEU LYS ASP SER SEQRES 22 A 803 SER LEU HIS THR LEU ASN SER SER TRP PHE GLN GLY LEU SEQRES 23 A 803 VAL GLN LEU SER VAL LEU ASP LEU SER GLU ASN PHE LEU SEQRES 24 A 803 TYR GLU SER ILE THR HIS THR ASN ALA PHE GLN ASN LEU SEQRES 25 A 803 THR ARG LEU ARG LYS LEU ASN LEU SER PHE ASN TYR ARG SEQRES 26 A 803 LYS LYS VAL SER PHE ALA ARG LEU HIS LEU ALA SER SER SEQRES 27 A 803 PHE LYS ASN LEU VAL SER LEU GLN GLU LEU ASN MET ASN SEQRES 28 A 803 GLY ILE PHE PHE ARG LEU LEU ASN LYS TYR THR LEU ARG SEQRES 29 A 803 TRP LEU ALA ASP LEU PRO LYS LEU HIS THR LEU HIS LEU SEQRES 30 A 803 GLN MET ASN PHE ILE ASN GLN ALA GLN LEU SER ILE PHE SEQRES 31 A 803 GLY THR PHE ARG ALA LEU ARG PHE VAL ASP LEU SER ASP SEQRES 32 A 803 ASN ARG ILE SER GLY PRO SER THR LEU SER GLU ALA THR SEQRES 33 A 803 PRO GLU GLU ALA ASP ASP ALA GLU GLN GLU GLU LEU LEU SEQRES 34 A 803 SER ALA ASP PRO HIS PRO ALA PRO LEU SER THR PRO ALA SEQRES 35 A 803 SER LYS ASN PHE MET ASP ARG CYS LYS ASN PHE LYS PHE SEQRES 36 A 803 THR MET ASP LEU SER ARG ASN ASN LEU VAL THR ILE LYS SEQRES 37 A 803 PRO GLU MET PHE VAL GLN LEU SER ARG LEU GLN CYS LEU SEQRES 38 A 803 SER LEU SER HIS ASN SER ILE ALA GLN ALA VAL ASN GLY SEQRES 39 A 803 SER GLN PHE LEU PRO LEU THR ASN LEU GLN VAL LEU ASP SEQRES 40 A 803 LEU SER HIS ASN LYS LEU ASP LEU TYR HIS TRP LYS SER SEQRES 41 A 803 PHE SER GLU LEU PRO GLN LEU GLN ALA LEU ASP LEU SER SEQRES 42 A 803 TYR ASN SER GLN PRO PHE SER MET LYS GLY ILE GLY HIS SEQRES 43 A 803 GLN PHE SER PHE VAL THR HIS LEU SER MET LEU GLN SER SEQRES 44 A 803 LEU SER LEU ALA HIS ASN ASP ILE HIS THR ARG VAL SER SEQRES 45 A 803 SER HIS LEU ASN SER ASN SER VAL ARG PHE LEU ASP PHE SEQRES 46 A 803 SER GLY ASN GLY MET GLY ARG MET TRP ASP GLU GLY GLY SEQRES 47 A 803 LEU TYR LEU HIS PHE PHE GLN GLY LEU SER GLY LEU LEU SEQRES 48 A 803 LYS LEU ASP LEU SER GLN ASN ASN LEU HIS ILE LEU ARG SEQRES 49 A 803 PRO GLN ASN LEU ASP ASN LEU PRO LYS SER LEU LYS LEU SEQRES 50 A 803 LEU SER LEU ARG ASP ASN TYR LEU SER PHE PHE ASN TRP SEQRES 51 A 803 THR SER LEU SER PHE LEU PRO ASN LEU GLU VAL LEU ASP SEQRES 52 A 803 LEU ALA GLY ASN GLN LEU LYS ALA LEU THR GLN GLY THR SEQRES 53 A 803 LEU PRO ASN GLY THR LEU LEU GLN LYS LEU ASP VAL SER SEQRES 54 A 803 SER ASN SER ILE VAL SER VAL VAL PRO ALA PHE PHE ALA SEQRES 55 A 803 LEU ALA VAL GLU LEU LYS GLU VAL ASN LEU SER HIS ASN SEQRES 56 A 803 ILE LEU LYS THR VAL ASP ARG SER TRP PHE GLY PRO ILE SEQRES 57 A 803 VAL MET GLN LEU THR VAL LEU ASP VAL ARG SER ASN PRO SEQRES 58 A 803 LEU HIS CYS ALA CYS GLY ALA ALA PHE VAL ASP LEU LEU SEQRES 59 A 803 LEU GLU VAL GLN THR LYS VAL PRO GLY LEU ALA ASN GLY SEQRES 60 A 803 VAL LYS CYS GLY SER PRO GLY GLN LEU GLN GLY ARG SER SEQRES 61 A 803 ILE PHE ALA GLN ASP LEU ARG LEU CYS LEU ASP GLU VAL SEQRES 62 A 803 LEU SER TRP ASP GLU PHE LEU VAL PRO ARG SEQRES 1 B 12 DC DC DT DG DG DA DT DG DG DG DA DA MODRES 3WPG ASN A 732 ASN GLYCOSYLATION SITE HET NAG A 901 14 HET SO4 A 902 5 HET SO4 A 903 5 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 B 101 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION FORMUL 3 NAG C8 H15 N O6 FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 HOH *77(H2 O) HELIX 1 1 PHE A 83 SER A 87 5 5 HELIX 2 2 THR A 118 MET A 122 5 5 HELIX 3 3 ASN A 300 PHE A 304 5 5 HELIX 4 4 GLU A 322 THR A 327 1 6 HELIX 5 5 ALA A 357 LEU A 363 5 7 HELIX 6 6 LEU A 384 ALA A 388 5 5 HELIX 7 7 LEU A 408 THR A 413 5 6 HELIX 8 8 LYS A 489 VAL A 494 5 6 HELIX 9 9 PHE A 569 LEU A 575 5 7 HELIX 10 10 GLY A 610 TRP A 615 1 6 HELIX 11 11 ARG A 645 ASN A 651 1 7 HELIX 12 12 ASN A 670 LEU A 677 5 8 HELIX 13 13 ASP A 742 GLN A 752 5 11 HELIX 14 14 ALA A 770 VAL A 778 1 9 HELIX 15 15 GLN A 779 VAL A 782 5 4 SHEET 1 A28 GLU A 36 LEU A 37 0 SHEET 2 A28 LEU A 42 ASP A 44 -1 O ASP A 44 N GLU A 36 SHEET 3 A28 ARG A 67 SER A 69 1 O SER A 69 N VAL A 43 SHEET 4 A28 GLN A 91 ASN A 93 1 O ASN A 93 N LEU A 68 SHEET 5 A28 GLU A 127 ASN A 129 1 O ASN A 129 N LEU A 92 SHEET 6 A28 ASN A 147 SER A 149 1 O SER A 149 N LEU A 128 SHEET 7 A28 VAL A 171 PHE A 173 1 O VAL A 171 N LEU A 148 SHEET 8 A28 HIS A 203 SER A 205 1 O HIS A 203 N LEU A 172 SHEET 9 A28 TYR A 224 LEU A 226 1 O LEU A 226 N LEU A 204 SHEET 10 A28 VAL A 248 ASP A 250 1 O ASP A 250 N LEU A 225 SHEET 11 A28 GLY A 288 VAL A 290 1 O GLY A 288 N LEU A 249 SHEET 12 A28 VAL A 312 ASP A 314 1 O ASP A 314 N LEU A 289 SHEET 13 A28 LYS A 338 ASN A 340 1 O ASN A 340 N LEU A 313 SHEET 14 A28 GLU A 368 ASN A 370 1 O ASN A 370 N LEU A 339 SHEET 15 A28 THR A 395 HIS A 397 1 O HIS A 397 N LEU A 369 SHEET 16 A28 PHE A 419 ASP A 421 1 O PHE A 419 N LEU A 396 SHEET 17 A28 THR A 477 ASP A 479 1 O ASP A 479 N VAL A 420 SHEET 18 A28 CYS A 501 SER A 503 1 O CYS A 501 N MET A 478 SHEET 19 A28 VAL A 526 ASP A 528 1 O ASP A 528 N LEU A 502 SHEET 20 A28 ALA A 550 ASP A 552 1 O ALA A 550 N LEU A 527 SHEET 21 A28 SER A 580 SER A 582 1 O SER A 580 N LEU A 551 SHEET 22 A28 PHE A 603 ASP A 605 1 O ASP A 605 N LEU A 581 SHEET 23 A28 LYS A 633 ASP A 635 1 O LYS A 633 N LEU A 604 SHEET 24 A28 LEU A 658 SER A 660 1 O LEU A 658 N LEU A 634 SHEET 25 A28 VAL A 682 ASP A 684 1 O VAL A 682 N LEU A 659 SHEET 26 A28 LYS A 706 ASP A 708 1 O LYS A 706 N LEU A 683 SHEET 27 A28 GLU A 730 ASN A 732 1 O GLU A 730 N LEU A 707 SHEET 28 A28 VAL A 755 ASP A 757 1 O ASP A 757 N VAL A 731 SHEET 1 B 2 HIS A 77 LEU A 78 0 SHEET 2 B 2 THR A 113 ILE A 114 1 O THR A 113 N LEU A 78 SHEET 1 C 2 VAL A 157 LEU A 158 0 SHEET 2 C 2 LYS A 189 VAL A 190 1 O LYS A 189 N LEU A 158 SHEET 1 D 2 LYS A 234 LEU A 235 0 SHEET 2 D 2 HIS A 274 LEU A 275 1 O HIS A 274 N LEU A 235 SHEET 1 E 2 LEU A 378 LEU A 379 0 SHEET 2 E 2 GLN A 405 ALA A 406 1 O GLN A 405 N LEU A 379 SHEET 1 F 2 ASN A 597 SER A 598 0 SHEET 2 F 2 GLY A 627 LEU A 628 1 O GLY A 627 N SER A 598 SHEET 1 G 2 LEU A 763 HIS A 764 0 SHEET 2 G 2 CYS A 791 SER A 793 1 O GLY A 792 N LEU A 763 SSBOND 1 CYS A 35 CYS A 45 1555 1555 2.03 SSBOND 2 CYS A 98 CYS A 110 1555 1555 2.03 SSBOND 3 CYS A 178 CYS A 184 1555 1555 2.03 SSBOND 4 CYS A 255 CYS A 268 1555 1555 2.03 SSBOND 5 CYS A 258 CYS A 265 1555 1555 2.04 SSBOND 6 CYS A 471 CYS A 501 1555 1555 2.03 SSBOND 7 CYS A 765 CYS A 791 1555 1555 2.03 SSBOND 8 CYS A 767 CYS A 810 1555 1555 2.03 LINK ND2 ASN A 732 C1 NAG A 901 1555 1555 1.51 CISPEP 1 LEU A 33 PRO A 34 0 2.45 CISPEP 2 THR A 101 GLY A 102 0 1.05 CISPEP 3 ARG A 470 CYS A 471 0 6.41 CISPEP 4 GLN A 695 GLY A 696 0 0.44 CISPEP 5 ASN A 700 GLY A 701 0 -5.54 CISPEP 6 SER A 793 PRO A 794 0 -1.71 CRYST1 71.230 123.860 130.440 90.00 90.00 90.00 P 21 21 21 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 0.014039 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007666 0.00000