HEADER HYDROLASE/RNA 23-MAY-13 4BPB TITLE STRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT RNA HELICASE DDX58; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 230-925; COMPND 5 SYNONYM: DEAD BOX PROTEIN 58, RETINOIC ACID-INDUCIBLE GENE 1 COMPND 6 PROTEIN, RIG-1, RETINOIC ACID-INDUCIBLE GENE I PROTEIN, RIG-I; COMPND 7 EC: 3.6.4.13; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'; COMPND 11 CHAIN: C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE-RNA COMPLEX, ADENOSINE TRIPHOSPHATE, DEAD-BOX RNA KEYWDS 2 HELICASES, DOUBLE-STRANDED, SIGNAL TRANSDUCTION EXPDTA X-RAY DIFFRACTION AUTHOR D.LUO,A.M.PYLE REVDAT 1 19-JUN-13 4BPB 0 JRNL AUTH D.LUO,S.C.DING,A.VELA,A.KOHLWAY,B.D.LINDENBACH,A.M.PYLE JRNL TITL STRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I. JRNL REF CELL(CAMBRIDGE,MASS.) V. 147 409 2011 JRNL REFN ISSN 0092-8674 JRNL PMID 22000018 JRNL DOI 10.1016/J.CELL.2011.09.023 REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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) : 2.584 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.928 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.02 REMARK 3 NUMBER OF REFLECTIONS : 25746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1978 REMARK 3 R VALUE (WORKING SET) : 0.1947 REMARK 3 FREE R VALUE : 0.2554 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1311 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 39.9324 - 5.3711 1.00 2926 148 0.1916 0.2264 REMARK 3 2 5.3711 - 4.2648 1.00 2770 152 0.1547 0.1965 REMARK 3 3 4.2648 - 3.7261 1.00 2756 151 0.1646 0.2537 REMARK 3 4 3.7261 - 3.3857 1.00 2699 152 0.1896 0.2691 REMARK 3 5 3.3857 - 3.1431 1.00 2739 126 0.2131 0.2751 REMARK 3 6 3.1431 - 2.9578 1.00 2670 160 0.2290 0.3238 REMARK 3 7 2.9578 - 2.8098 1.00 2675 148 0.2534 0.3026 REMARK 3 8 2.8098 - 2.6875 0.99 2722 133 0.2815 0.3713 REMARK 3 9 2.6875 - 2.5840 0.93 2478 141 0.2752 0.3288 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) : 0.35 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 5566 REMARK 3 ANGLE : 0.735 7622 REMARK 3 CHIRALITY : 0.053 879 REMARK 3 PLANARITY : 0.003 894 REMARK 3 DIHEDRAL : 13.670 2102 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 236 THROUGH 455 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3498 13.3541 16.4757 REMARK 3 T TENSOR REMARK 3 T11: 0.1081 T22: 0.1363 REMARK 3 T33: 0.1894 T12: 0.0052 REMARK 3 T13: 0.0058 T23: 0.0947 REMARK 3 L TENSOR REMARK 3 L11: 1.4450 L22: 1.8883 REMARK 3 L33: 2.1786 L12: 0.3061 REMARK 3 L13: -0.3296 L23: -0.2842 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: -0.1837 S13: -0.1458 REMARK 3 S21: 0.0504 S22: 0.0573 S23: -0.1482 REMARK 3 S31: 0.0077 S32: 0.2033 S33: -0.0238 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 456 THROUGH 795 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0759 -18.8865 22.6294 REMARK 3 T TENSOR REMARK 3 T11: 0.3222 T22: 0.3385 REMARK 3 T33: 0.3062 T12: -0.0892 REMARK 3 T13: -0.0009 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 0.3994 L22: 2.0049 REMARK 3 L33: 1.1576 L12: 0.2776 REMARK 3 L13: -0.4818 L23: -0.7375 REMARK 3 S TENSOR REMARK 3 S11: -0.1312 S12: 0.0317 S13: -0.0953 REMARK 3 S21: -0.0006 S22: 0.0173 S23: 0.1400 REMARK 3 S31: 0.4210 S32: -0.0668 S33: 0.0953 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 796 THROUGH 927 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8237 7.1057 49.8510 REMARK 3 T TENSOR REMARK 3 T11: 0.4782 T22: 0.4506 REMARK 3 T33: 0.2925 T12: 0.0269 REMARK 3 T13: 0.0891 T23: 0.0137 REMARK 3 L TENSOR REMARK 3 L11: 2.7605 L22: 2.7936 REMARK 3 L33: 3.7796 L12: 0.1736 REMARK 3 L13: -0.7078 L23: -0.0007 REMARK 3 S TENSOR REMARK 3 S11: -0.1373 S12: -0.0619 S13: -0.4216 REMARK 3 S21: 0.3693 S22: -0.3451 S23: 0.0717 REMARK 3 S31: 0.1384 S32: -0.0524 S33: 0.4530 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN C AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.6674 1.9374 28.0065 REMARK 3 T TENSOR REMARK 3 T11: 0.3971 T22: 0.5065 REMARK 3 T33: 0.4262 T12: -0.0960 REMARK 3 T13: -0.1012 T23: 0.1261 REMARK 3 L TENSOR REMARK 3 L11: 3.2411 L22: 1.6438 REMARK 3 L33: 0.7609 L12: -0.8778 REMARK 3 L13: -1.0545 L23: -0.4935 REMARK 3 S TENSOR REMARK 3 S11: 0.2382 S12: 0.2294 S13: -0.4774 REMARK 3 S21: -0.3634 S22: 0.3828 S23: 0.7391 REMARK 3 S31: 0.3567 S32: -1.1910 S33: -0.3001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN D AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.5285 0.4041 30.8073 REMARK 3 T TENSOR REMARK 3 T11: 0.3373 T22: 0.5952 REMARK 3 T33: 0.6783 T12: 0.0021 REMARK 3 T13: -0.2947 T23: 0.4889 REMARK 3 L TENSOR REMARK 3 L11: 1.2584 L22: 0.5086 REMARK 3 L33: 0.6101 L12: 0.4751 REMARK 3 L13: 0.0570 L23: 0.4691 REMARK 3 S TENSOR REMARK 3 S11: -0.0014 S12: -0.0242 S13: -0.1958 REMARK 3 S21: -0.2496 S22: 0.5078 S23: 0.5287 REMARK 3 S31: -0.1244 S32: -0.6102 S33: 0.1253 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BETTER REFINEMENT OF PDB ENTRY 2YKG REMARK 4 REMARK 4 4BPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-13. REMARK 100 THE PDBE ID CODE IS EBI-57001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 315) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25750 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90 REMARK 200 RESOLUTION RANGE LOW (A) : 45.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.56 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.2 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.22 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.6 REMARK 200 R MERGE FOR SHELL (I) : 0.61 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.56 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE, PH 9.0, 22.5 % REMARK 280 POLYETHYLENE GLYCOL 6,000 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 23.80900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 109.91250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.10400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 109.91250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.80900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.10400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 SER A 230 REMARK 465 GLU A 231 REMARK 465 VAL A 232 REMARK 465 SER A 233 REMARK 465 ASP A 234 REMARK 465 THR A 235 REMARK 465 PHE A 523 REMARK 465 GLN A 524 REMARK 465 MET A 525 REMARK 465 PRO A 526 REMARK 465 ASP A 527 REMARK 465 LYS A 528 REMARK 465 LEU A 661 REMARK 465 THR A 662 REMARK 465 GLY A 663 REMARK 465 ARG A 664 REMARK 465 GLY A 665 REMARK 465 LYS A 666 REMARK 465 THR A 667 REMARK 465 ASN A 668 REMARK 465 GLN A 669 REMARK 465 ASN A 670 REMARK 465 THR A 671 REMARK 465 PHE A 671A REMARK 465 PHE A 671B REMARK 465 GLY A 672 REMARK 465 MET A 673 REMARK 465 THR A 674 REMARK 465 LEU A 675 REMARK 465 PRO A 676 REMARK 465 ALA A 677 REMARK 465 GLN A 678 REMARK 465 LYS A 679 REMARK 465 CYS A 680 REMARK 465 ILE A 681 REMARK 465 LEU A 682 REMARK 465 ASP A 683 REMARK 465 ALA A 684 REMARK 465 PHE A 685 REMARK 465 LYS A 686 REMARK 465 ALA A 687 REMARK 465 SER A 688 REMARK 465 GLY A 689 REMARK 465 ASP A 690 REMARK 465 GLU A 702 REMARK 465 GLY A 703 REMARK 465 ILE A 704 REMARK 465 ASP A 705 REMARK 465 ILE A 706 REMARK 465 GLY A 719 REMARK 465 ASN A 720 REMARK 465 ILE A 725 REMARK 465 GLN A 726 REMARK 465 THR A 727 REMARK 465 ARG A 728 REMARK 465 GLY A 729 REMARK 465 ARG A 730 REMARK 465 GLY A 731 REMARK 465 ARG A 732 REMARK 465 ALA A 733 REMARK 465 GLU A 922 REMARK 465 MET A 923 REMARK 465 SER A 924 REMARK 465 LYS A 925 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 236 CG OD1 ND2 REMARK 470 GLU A 315 CG CD OE1 OE2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 ASN A 331 CG OD1 ND2 REMARK 470 VAL A 332 CG1 CG2 REMARK 470 GLU A 335 CG CD OE1 OE2 REMARK 470 LYS A 356 CG CD CE NZ REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 THR A 367 CG2 REMARK 470 ASP A 416 CG OD1 OD2 REMARK 470 LYS A 418 CG CD CE NZ REMARK 470 ASP A 421 CG OD1 OD2 REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 GLU A 464 CG CD OE1 OE2 REMARK 470 GLN A 507 CG CD OE1 NE2 REMARK 470 ASP A 529 CG OD1 OD2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 GLU A 531 CG CD OE1 OE2 REMARK 470 ARG A 575 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 580 CG OD1 OD2 REMARK 470 GLU A 612 CG CD OE1 OE2 REMARK 470 HIS A 623 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 624 CG CD1 CD2 REMARK 470 GLU A 627 CG CD OE1 OE2 REMARK 470 HIS A 691 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 701 CG OD1 OD2 REMARK 470 GLN A 708 CG CD OE1 NE2 REMARK 470 VAL A 718 CG1 CG2 REMARK 470 VAL A 721 CG1 CG2 REMARK 470 ILE A 722 CG1 CG2 CD1 REMARK 470 LYS A 723 CG CD CE NZ REMARK 470 MET A 724 CG SD CE REMARK 470 ARG A 734 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 796 CG CD CE NZ REMARK 470 LYS A 798 CG CD CE NZ REMARK 470 VAL A 800 CG1 CG2 REMARK 470 ASP A 802 CG OD1 OD2 REMARK 470 LYS A 807 NZ REMARK 470 ASP A 828 CG OD1 OD2 REMARK 470 LYS A 878 NZ REMARK 470 GLU A 914 CD OE1 OE2 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 CYS A 268 CA CB SG 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 O ARG A 767 OG1 THR A 770 2.20 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 LEU A 237 37.13 -93.48 REMARK 500 PRO A 240 85.92 -45.85 REMARK 500 PHE A 314 30.14 -97.78 REMARK 500 THR A 328 -85.48 -78.40 REMARK 500 LYS A 379 -124.48 54.93 REMARK 500 SER A 398 77.02 -150.21 REMARK 500 SER A 399 -59.10 43.62 REMARK 500 ASP A 416 40.87 -85.67 REMARK 500 LYS A 443 -53.03 -127.62 REMARK 500 TYR A 454 92.88 -68.63 REMARK 500 ALA A 519 30.91 -81.36 REMARK 500 CYS A 520 67.12 -164.31 REMARK 500 ALA A 558 -137.85 -103.45 REMARK 500 ALA A 576 -82.04 -61.51 REMARK 500 LEU A 624 -80.37 -99.22 REMARK 500 ASN A 692 34.05 -83.49 REMARK 500 ASP A 828 -17.26 66.77 REMARK 500 SER A 855 -47.32 -132.95 REMARK 500 GLN A 867 10.34 -67.48 REMARK 500 CYS A 869 -76.99 -88.60 REMARK 500 THR A 881 -2.72 63.55 REMARK 500 THR A 899 -134.85 -84.80 REMARK 500 PRO A 920 75.54 -63.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 927 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 813 SG REMARK 620 2 CYS A 810 SG 109.7 REMARK 620 3 CYS A 864 SG 108.6 110.0 REMARK 620 4 CYS A 869 SG 109.3 108.9 110.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 927 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1923 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YKG RELATED DB: PDB REMARK 900 STRUCTURAL INSIGHTS INTO RNA RECOGNITION BY RIG-I DBREF 4BPB A 230 925 UNP O95786 DDX58_HUMAN 230 925 DBREF 4BPB C 1 10 PDB 4BPB 4BPB 1 10 DBREF 4BPB D 1 10 PDB 4BPB 4BPB 1 10 SEQADV 4BPB ASN A 306 UNP O95786 GLN 306 CONFLICT SEQADV 4BPB THR A 419 UNP O95786 ASN 419 CONFLICT SEQADV 4BPB PHE A 671A UNP O95786 INSERTION SEQADV 4BPB PHE A 671B UNP O95786 INSERTION SEQADV 4BPB ASP A 828 UNP O95786 GLU 828 CONFLICT SEQRES 1 A 698 SER GLU VAL SER ASP THR ASN LEU TYR SER PRO PHE LYS SEQRES 2 A 698 PRO ARG ASN TYR GLN LEU GLU LEU ALA LEU PRO ALA MET SEQRES 3 A 698 LYS GLY LYS ASN THR ILE ILE CYS ALA PRO THR GLY CYS SEQRES 4 A 698 GLY LYS THR PHE VAL SER LEU LEU ILE CYS GLU HIS HIS SEQRES 5 A 698 LEU LYS LYS PHE PRO GLN GLY GLN LYS GLY LYS VAL VAL SEQRES 6 A 698 PHE PHE ALA ASN GLN ILE PRO VAL TYR GLU GLN ASN LYS SEQRES 7 A 698 SER VAL PHE SER LYS TYR PHE GLU ARG HIS GLY TYR ARG SEQRES 8 A 698 VAL THR GLY ILE SER GLY ALA THR ALA GLU ASN VAL PRO SEQRES 9 A 698 VAL GLU GLN ILE VAL GLU ASN ASN ASP ILE ILE ILE LEU SEQRES 10 A 698 THR PRO GLN ILE LEU VAL ASN ASN LEU LYS LYS GLY THR SEQRES 11 A 698 ILE PRO SER LEU SER ILE PHE THR LEU MET ILE PHE ASP SEQRES 12 A 698 GLU CYS HIS ASN THR SER LYS GLN HIS PRO TYR ASN MET SEQRES 13 A 698 ILE MET PHE ASN TYR LEU ASP GLN LYS LEU GLY GLY SER SEQRES 14 A 698 SER GLY PRO LEU PRO GLN VAL ILE GLY LEU THR ALA SER SEQRES 15 A 698 VAL GLY VAL GLY ASP ALA LYS THR THR ASP GLU ALA LEU SEQRES 16 A 698 ASP TYR ILE CYS LYS LEU CYS ALA SER LEU ASP ALA SER SEQRES 17 A 698 VAL ILE ALA THR VAL LYS HIS ASN LEU GLU GLU LEU GLU SEQRES 18 A 698 GLN VAL VAL TYR LYS PRO GLN LYS PHE PHE ARG LYS VAL SEQRES 19 A 698 GLU SER ARG ILE SER ASP LYS PHE LYS TYR ILE ILE ALA SEQRES 20 A 698 GLN LEU MET ARG ASP THR GLU SER LEU ALA LYS ARG ILE SEQRES 21 A 698 CYS LYS ASP LEU GLU ASN LEU SER GLN ILE GLN ASN ARG SEQRES 22 A 698 GLU PHE GLY THR GLN LYS TYR GLU GLN TRP ILE VAL THR SEQRES 23 A 698 VAL GLN LYS ALA CYS MET VAL PHE GLN MET PRO ASP LYS SEQRES 24 A 698 ASP GLU GLU SER ARG ILE CYS LYS ALA LEU PHE LEU TYR SEQRES 25 A 698 THR SER HIS LEU ARG LYS TYR ASN ASP ALA LEU ILE ILE SEQRES 26 A 698 SER GLU HIS ALA ARG MET LYS ASP ALA LEU ASP TYR LEU SEQRES 27 A 698 LYS ASP PHE PHE SER ASN VAL ARG ALA ALA GLY PHE ASP SEQRES 28 A 698 GLU ILE GLU GLN ASP LEU THR GLN ARG PHE GLU GLU LYS SEQRES 29 A 698 LEU GLN GLU LEU GLU SER VAL SER ARG ASP PRO SER ASN SEQRES 30 A 698 GLU ASN PRO LYS LEU GLU ASP LEU CYS PHE ILE LEU GLN SEQRES 31 A 698 GLU GLU TYR HIS LEU ASN PRO GLU THR ILE THR ILE LEU SEQRES 32 A 698 PHE VAL LYS THR ARG ALA LEU VAL ASP ALA LEU LYS ASN SEQRES 33 A 698 TRP ILE GLU GLY ASN PRO LYS LEU SER PHE LEU LYS PRO SEQRES 34 A 698 GLY ILE LEU THR GLY ARG GLY LYS THR ASN GLN ASN THR SEQRES 35 A 698 PHE PHE GLY MET THR LEU PRO ALA GLN LYS CYS ILE LEU SEQRES 36 A 698 ASP ALA PHE LYS ALA SER GLY ASP HIS ASN ILE LEU ILE SEQRES 37 A 698 ALA THR SER VAL ALA ASP GLU GLY ILE ASP ILE ALA GLN SEQRES 38 A 698 CYS ASN LEU VAL ILE LEU TYR GLU TYR VAL GLY ASN VAL SEQRES 39 A 698 ILE LYS MET ILE GLN THR ARG GLY ARG GLY ARG ALA ARG SEQRES 40 A 698 GLY SER LYS CYS PHE LEU LEU THR SER ASN ALA GLY VAL SEQRES 41 A 698 ILE GLU LYS GLU GLN ILE ASN MET TYR LYS GLU LYS MET SEQRES 42 A 698 MET ASN ASP SER ILE LEU ARG LEU GLN THR TRP ASP GLU SEQRES 43 A 698 ALA VAL PHE ARG GLU LYS ILE LEU HIS ILE GLN THR HIS SEQRES 44 A 698 GLU LYS PHE ILE ARG ASP SER GLN GLU LYS PRO LYS PRO SEQRES 45 A 698 VAL PRO ASP LYS GLU ASN LYS LYS LEU LEU CYS ARG LYS SEQRES 46 A 698 CYS LYS ALA LEU ALA CYS TYR THR ALA ASP VAL ARG VAL SEQRES 47 A 698 ILE GLU ASP CYS HIS TYR THR VAL LEU GLY ASP ALA PHE SEQRES 48 A 698 LYS GLU CYS PHE VAL SER ARG PRO HIS PRO LYS PRO LYS SEQRES 49 A 698 GLN PHE SER SER PHE GLU LYS ARG ALA LYS ILE PHE CYS SEQRES 50 A 698 ALA ARG GLN ASN CYS SER HIS ASP TRP GLY ILE HIS VAL SEQRES 51 A 698 LYS TYR LYS THR PHE GLU ILE PRO VAL ILE LYS ILE GLU SEQRES 52 A 698 SER PHE VAL VAL GLU ASP ILE ALA THR GLY VAL GLN THR SEQRES 53 A 698 LEU TYR SER LYS TRP LYS ASP PHE HIS PHE GLU LYS ILE SEQRES 54 A 698 PRO PHE ASP PRO ALA GLU MET SER LYS SEQRES 1 C 10 G C G C G C G C G C SEQRES 1 D 10 G C G C G C G C G C HET ZN A 927 1 HET SO4 A1923 5 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 2 SO4 O4 S 2- FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *107(H2 O) HELIX 1 1 ARG A 244 LYS A 256 1 13 HELIX 2 2 GLY A 269 LYS A 284 1 16 HELIX 3 3 GLN A 299 PHE A 314 1 16 HELIX 4 4 PRO A 333 ASN A 340 1 8 HELIX 5 5 THR A 347 LYS A 357 1 11 HELIX 6 6 SER A 362 PHE A 366 5 5 HELIX 7 7 CYS A 374 THR A 377 5 4 HELIX 8 8 HIS A 381 GLY A 396 1 16 HELIX 9 9 THR A 419 LEU A 434 1 16 HELIX 10 10 ASN A 445 GLN A 451 1 7 HELIX 11 11 ASP A 469 CYS A 490 1 22 HELIX 12 12 ASP A 492 LEU A 496 5 5 HELIX 13 13 THR A 506 ALA A 519 1 14 HELIX 14 14 GLU A 530 ALA A 558 1 29 HELIX 15 15 ARG A 559 ALA A 577 1 19 HELIX 16 16 ASP A 580 GLU A 592 1 13 HELIX 17 17 LYS A 593 ASP A 603 1 11 HELIX 18 18 ASN A 608 HIS A 623 1 16 HELIX 19 19 THR A 636 GLY A 649 1 14 HELIX 20 20 ASN A 650 SER A 654 5 5 HELIX 21 21 ASN A 744 TRP A 771 1 28 HELIX 22 22 ASP A 772 GLN A 794 1 23 HELIX 23 23 LYS A 907 PHE A 911 5 5 SHEET 1 AA 7 VAL A 321 ILE A 324 0 SHEET 2 AA 7 ILE A 343 LEU A 346 1 O ILE A 343 N THR A 322 SHEET 3 AA 7 VAL A 293 PHE A 296 1 O VAL A 293 N ILE A 344 SHEET 4 AA 7 LEU A 368 ASP A 372 1 O LEU A 368 N VAL A 294 SHEET 5 AA 7 GLN A 404 THR A 409 1 O GLN A 404 N MET A 369 SHEET 6 AA 7 THR A 260 CYS A 263 1 O THR A 260 N GLY A 407 SHEET 7 AA 7 VAL A 438 ALA A 440 1 O VAL A 438 N ILE A 261 SHEET 1 AB 6 GLN A 457 LYS A 462 0 SHEET 2 AB 6 LYS A 737 THR A 742 1 O CYS A 738 N PHE A 459 SHEET 3 AB 6 LEU A 711 TYR A 715 1 O VAL A 712 N PHE A 739 SHEET 4 AB 6 THR A 630 PHE A 633 1 O ILE A 631 N ILE A 713 SHEET 5 AB 6 ILE A 695 SER A 698 1 O ALA A 696 N LEU A 632 SHEET 6 AB 6 PRO A 658 GLY A 659 1 O GLY A 659 N THR A 697 SHEET 1 AC 4 LEU A 816 TYR A 819 0 SHEET 2 AC 4 LYS A 806 CYS A 810 -1 O LEU A 808 N CYS A 818 SHEET 3 AC 4 PHE A 892 ASP A 896 -1 O VAL A 893 N LEU A 809 SHEET 4 AC 4 GLN A 902 LEU A 904 -1 O THR A 903 N VAL A 894 SHEET 1 AD 3 HIS A 830 VAL A 833 0 SHEET 2 AD 3 VAL A 823 ILE A 826 -1 O ARG A 824 N THR A 832 SHEET 3 AD 3 ILE A 916 PRO A 917 1 O ILE A 916 N VAL A 825 SHEET 1 AE 4 PHE A 842 PRO A 846 0 SHEET 2 AE 4 GLU A 857 CYS A 864 -1 O LYS A 861 N ARG A 845 SHEET 3 AE 4 ASP A 872 TYR A 879 -1 N TRP A 873 O ILE A 862 SHEET 4 AE 4 PHE A 882 ILE A 887 -1 O PHE A 882 N TYR A 879 SSBOND 1 CYS A 520 CYS A 535 1555 1555 2.03 LINK ZN ZN A 927 SG CYS A 813 1555 1555 2.24 LINK ZN ZN A 927 SG CYS A 810 1555 1555 2.25 LINK ZN ZN A 927 SG CYS A 864 1555 1555 2.26 LINK ZN ZN A 927 SG CYS A 869 1555 1555 2.25 CISPEP 1 ALA A 329 GLU A 330 0 2.59 SITE 1 AC1 4 CYS A 810 CYS A 813 CYS A 864 CYS A 869 SITE 1 AC2 6 THR A 266 GLY A 267 CYS A 268 GLY A 269 SITE 2 AC2 6 LYS A 270 HOH A2030 CRYST1 47.618 76.208 219.825 90.00 90.00 90.00 P 21 21 21 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 0.021000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004549 0.00000