HEADER HYDROLASE/RNA 17-JUN-12 4AY2 TITLE CAPTURING 5' TRI-PHOSPHORYLATED RNA DUPLEX BY RIG-I COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT RNA HELICASE DDX58; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 239-925; COMPND 5 SYNONYM: DDX58, DEAD BOX PROTEIN 58, RIG-I-LIKE RECEPTOR 1, RLR-1, COMPND 6 RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN, RIG-1, RETINOIC ACID- COMPND 7 INDUCIBLE GENE I PROTEIN, RIG-I; COMPND 8 EC: 3.6.4.13; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-R-PPP(GP*GP*CP*GP*CP*GP*GP*CP*UP*UP*CP*GP*GP*CP COMPND 11 *CP*GP*CP*GP*CP*C)-3'; COMPND 12 CHAIN: C; COMPND 13 SYNONYM: 5' TRI-PHOSPHORYLATED RNA; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS HYDROLASE-RNA COMPLEX, INNATE IMMUNITY EXPDTA X-RAY DIFFRACTION AUTHOR D.LUO,A.M.PYLE REVDAT 4 20-DEC-23 4AY2 1 REMARK LINK REVDAT 3 28-NOV-12 4AY2 1 JRNL REVDAT 2 21-NOV-12 4AY2 1 JRNL REVDAT 1 03-OCT-12 4AY2 0 JRNL AUTH D.LUO,A.KOHLWAY,A.VELA,A.M.PYLE JRNL TITL VISUALIZING THE DETERMINANTS OF VIRAL RNA RECOGNITION BY JRNL TITL 2 INNATE IMMUNE SENSOR RIG-I. JRNL REF STRUCTURE V. 20 1983 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 23022350 JRNL DOI 10.1016/J.STR.2012.08.029 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 19224 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1036 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1362 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5007 REMARK 3 NUCLEIC ACID ATOMS : 436 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : -1.97000 REMARK 3 B33 (A**2) : 1.66000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.440 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.318 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 33.592 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.861 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5624 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7701 ; 1.135 ; 1.912 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 623 ; 5.112 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 231 ;35.820 ;24.675 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 929 ;16.171 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;12.617 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 860 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4012 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : 4 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 239 A 455 REMARK 3 ORIGIN FOR THE GROUP (A): -8.5218 13.4427 -16.4463 REMARK 3 T TENSOR REMARK 3 T11: 0.0145 T22: 0.1924 REMARK 3 T33: 0.0454 T12: -0.0243 REMARK 3 T13: -0.0067 T23: -0.0670 REMARK 3 L TENSOR REMARK 3 L11: 3.3372 L22: 3.2522 REMARK 3 L33: 3.4686 L12: -1.0852 REMARK 3 L13: -0.1918 L23: -0.1778 REMARK 3 S TENSOR REMARK 3 S11: -0.0884 S12: 0.3858 S13: -0.0901 REMARK 3 S21: -0.1384 S22: 0.0504 S23: 0.1964 REMARK 3 S31: 0.1106 S32: -0.2415 S33: 0.0380 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 : A 456 A 798 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4813 -18.8195 -22.6639 REMARK 3 T TENSOR REMARK 3 T11: 0.2739 T22: 0.4350 REMARK 3 T33: 0.2653 T12: 0.0288 REMARK 3 T13: 0.0287 T23: 0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.2789 L22: 2.6365 REMARK 3 L33: 0.5736 L12: -0.5165 REMARK 3 L13: -0.1524 L23: 1.0838 REMARK 3 S TENSOR REMARK 3 S11: -0.0239 S12: -0.0274 S13: -0.1453 REMARK 3 S21: 0.0234 S22: -0.0369 S23: 0.1066 REMARK 3 S31: 0.1616 S32: -0.0286 S33: 0.0609 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 799 A 930 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8463 7.0072 -50.1809 REMARK 3 T TENSOR REMARK 3 T11: 0.4565 T22: 0.4888 REMARK 3 T33: 0.1830 T12: 0.0135 REMARK 3 T13: 0.0639 T23: 0.0344 REMARK 3 L TENSOR REMARK 3 L11: 8.0691 L22: 5.7236 REMARK 3 L33: 8.4498 L12: 0.2482 REMARK 3 L13: -1.9796 L23: -0.2077 REMARK 3 S TENSOR REMARK 3 S11: -0.0156 S12: 0.0136 S13: -0.4002 REMARK 3 S21: -0.6326 S22: -0.4104 S23: -0.1591 REMARK 3 S31: 0.1579 S32: 0.1970 S33: 0.4260 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 20 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6204 0.8647 -30.3065 REMARK 3 T TENSOR REMARK 3 T11: 0.3203 T22: 0.5660 REMARK 3 T33: 0.4374 T12: 0.0774 REMARK 3 T13: -0.0650 T23: -0.1795 REMARK 3 L TENSOR REMARK 3 L11: 4.4888 L22: 5.8158 REMARK 3 L33: 3.7474 L12: -3.5846 REMARK 3 L13: 0.1585 L23: -0.4015 REMARK 3 S TENSOR REMARK 3 S11: 0.1553 S12: 0.9068 S13: -0.5263 REMARK 3 S21: 0.3016 S22: -0.3914 S23: -0.5629 REMARK 3 S31: 0.3220 S32: 0.9499 S33: 0.2361 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: U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4AY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052934. 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 : NULL 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-C 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 REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20333 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.83000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 2YKG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 23.87250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 110.61100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.07800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 110.61100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.87250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.07800 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: 3690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.3 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 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 239 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 ASP A 529 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 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 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 VAL A 721 REMARK 465 ILE A 722 REMARK 465 LYS A 723 REMARK 465 MET A 724 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 ARG A 734 REMARK 465 GLY A 735 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 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 455 CG CD CE NZ REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 GLU A 531 CG CD OE1 OE2 REMARK 470 SER A 654 OG REMARK 470 LYS A 657 CG CD CE NZ 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 GLU A 795 CG CD OE1 OE2 REMARK 470 LYS A 796 CG CD CE NZ REMARK 470 LYS A 798 CG CD CE NZ REMARK 470 LYS A 812 CG CD CE NZ REMARK 470 GLN A 867 CG CD OE1 NE2 REMARK 470 ASN A 868 CG OD1 ND2 REMARK 470 GLU A 914 CG CD OE1 OE2 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 OE1 GLN A 451 O HOH A 2031 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GTP C 1 O3' G C 2 P 0.134 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 G C 2 O3' - P - O5' ANGL. DEV. = -12.9 DEGREES REMARK 500 G C 2 O3' - P - OP1 ANGL. DEV. = 9.7 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 PHE A 314 34.76 -96.98 REMARK 500 ASN A 331 39.88 -76.93 REMARK 500 HIS A 375 -9.95 -58.87 REMARK 500 LYS A 379 -129.90 54.51 REMARK 500 SER A 411 113.29 -167.78 REMARK 500 ASP A 416 31.70 -94.67 REMARK 500 ASP A 492 36.31 -87.07 REMARK 500 ALA A 558 -136.13 -108.80 REMARK 500 ALA A 577 19.29 -164.92 REMARK 500 PHE A 579 55.63 -149.37 REMARK 500 ASN A 625 94.52 -166.75 REMARK 500 GLU A 627 32.18 -81.49 REMARK 500 ASP A 690 -47.35 -132.72 REMARK 500 ASN A 692 74.62 -170.09 REMARK 500 GLN A 794 50.12 -92.97 REMARK 500 LYS A 796 -71.65 -54.46 REMARK 500 VAL A 800 104.55 60.20 REMARK 500 ALA A 817 -68.48 -90.55 REMARK 500 ASP A 828 -36.88 66.75 REMARK 500 SER A 854 -105.46 55.27 REMARK 500 GLN A 867 82.98 -64.84 REMARK 500 CYS A 869 -87.74 -75.30 REMARK 500 ASP A 872 99.66 -59.96 REMARK 500 LYS A 880 -87.06 50.28 REMARK 500 HIS A 912 78.01 -111.19 REMARK 500 GLU A 914 78.37 -56.83 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 A1923 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 810 SG REMARK 620 2 CYS A 813 SG 118.8 REMARK 620 3 CYS A 864 SG 113.8 121.1 REMARK 620 4 CYS A 869 SG 87.7 107.6 98.9 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 1923 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1924 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1925 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 4AY2 A 239 925 UNP O95786 DDX58_HUMAN 239 925 DBREF 4AY2 C 1 20 PDB 4AY2 4AY2 1 20 SEQADV 4AY2 ASN A 306 UNP O95786 GLN 306 CONFLICT SEQADV 4AY2 ASP A 828 UNP O95786 GLU 828 CONFLICT SEQRES 1 A 687 SER PRO PHE LYS PRO ARG ASN TYR GLN LEU GLU LEU ALA SEQRES 2 A 687 LEU PRO ALA MET LYS GLY LYS ASN THR ILE ILE CYS ALA SEQRES 3 A 687 PRO THR GLY CYS GLY LYS THR PHE VAL SER LEU LEU ILE SEQRES 4 A 687 CYS GLU HIS HIS LEU LYS LYS PHE PRO GLN GLY GLN LYS SEQRES 5 A 687 GLY LYS VAL VAL PHE PHE ALA ASN GLN ILE PRO VAL TYR SEQRES 6 A 687 GLU GLN ASN LYS SER VAL PHE SER LYS TYR PHE GLU ARG SEQRES 7 A 687 HIS GLY TYR ARG VAL THR GLY ILE SER GLY ALA THR ALA SEQRES 8 A 687 GLU ASN VAL PRO VAL GLU GLN ILE VAL GLU ASN ASN ASP SEQRES 9 A 687 ILE ILE ILE LEU THR PRO GLN ILE LEU VAL ASN ASN LEU SEQRES 10 A 687 LYS LYS GLY THR ILE PRO SER LEU SER ILE PHE THR LEU SEQRES 11 A 687 MET ILE PHE ASP GLU CYS HIS ASN THR SER LYS GLN HIS SEQRES 12 A 687 PRO TYR ASN MET ILE MET PHE ASN TYR LEU ASP GLN LYS SEQRES 13 A 687 LEU GLY GLY SER SER GLY PRO LEU PRO GLN VAL ILE GLY SEQRES 14 A 687 LEU THR ALA SER VAL GLY VAL GLY ASP ALA LYS ASN THR SEQRES 15 A 687 ASP GLU ALA LEU ASP TYR ILE CYS LYS LEU CYS ALA SER SEQRES 16 A 687 LEU ASP ALA SER VAL ILE ALA THR VAL LYS HIS ASN LEU SEQRES 17 A 687 GLU GLU LEU GLU GLN VAL VAL TYR LYS PRO GLN LYS PHE SEQRES 18 A 687 PHE ARG LYS VAL GLU SER ARG ILE SER ASP LYS PHE LYS SEQRES 19 A 687 TYR ILE ILE ALA GLN LEU MET ARG ASP THR GLU SER LEU SEQRES 20 A 687 ALA LYS ARG ILE CYS LYS ASP LEU GLU ASN LEU SER GLN SEQRES 21 A 687 ILE GLN ASN ARG GLU PHE GLY THR GLN LYS TYR GLU GLN SEQRES 22 A 687 TRP ILE VAL THR VAL GLN LYS ALA CYS MET VAL PHE GLN SEQRES 23 A 687 MET PRO ASP LYS ASP GLU GLU SER ARG ILE CYS LYS ALA SEQRES 24 A 687 LEU PHE LEU TYR THR SER HIS LEU ARG LYS TYR ASN ASP SEQRES 25 A 687 ALA LEU ILE ILE SER GLU HIS ALA ARG MET LYS ASP ALA SEQRES 26 A 687 LEU ASP TYR LEU LYS ASP PHE PHE SER ASN VAL ARG ALA SEQRES 27 A 687 ALA GLY PHE ASP GLU ILE GLU GLN ASP LEU THR GLN ARG SEQRES 28 A 687 PHE GLU GLU LYS LEU GLN GLU LEU GLU SER VAL SER ARG SEQRES 29 A 687 ASP PRO SER ASN GLU ASN PRO LYS LEU GLU ASP LEU CYS SEQRES 30 A 687 PHE ILE LEU GLN GLU GLU TYR HIS LEU ASN PRO GLU THR SEQRES 31 A 687 ILE THR ILE LEU PHE VAL LYS THR ARG ALA LEU VAL ASP SEQRES 32 A 687 ALA LEU LYS ASN TRP ILE GLU GLY ASN PRO LYS LEU SER SEQRES 33 A 687 PHE LEU LYS PRO GLY ILE LEU THR GLY ARG GLY LYS THR SEQRES 34 A 687 ASN GLN ASN THR GLY MET THR LEU PRO ALA GLN LYS CYS SEQRES 35 A 687 ILE LEU ASP ALA PHE LYS ALA SER GLY ASP HIS ASN ILE SEQRES 36 A 687 LEU ILE ALA THR SER VAL ALA ASP GLU GLY ILE ASP ILE SEQRES 37 A 687 ALA GLN CYS ASN LEU VAL ILE LEU TYR GLU TYR VAL GLY SEQRES 38 A 687 ASN VAL ILE LYS MET ILE GLN THR ARG GLY ARG GLY ARG SEQRES 39 A 687 ALA ARG GLY SER LYS CYS PHE LEU LEU THR SER ASN ALA SEQRES 40 A 687 GLY VAL ILE GLU LYS GLU GLN ILE ASN MET TYR LYS GLU SEQRES 41 A 687 LYS MET MET ASN ASP SER ILE LEU ARG LEU GLN THR TRP SEQRES 42 A 687 ASP GLU ALA VAL PHE ARG GLU LYS ILE LEU HIS ILE GLN SEQRES 43 A 687 THR HIS GLU LYS PHE ILE ARG ASP SER GLN GLU LYS PRO SEQRES 44 A 687 LYS PRO VAL PRO ASP LYS GLU ASN LYS LYS LEU LEU CYS SEQRES 45 A 687 ARG LYS CYS LYS ALA LEU ALA CYS TYR THR ALA ASP VAL SEQRES 46 A 687 ARG VAL ILE GLU ASP CYS HIS TYR THR VAL LEU GLY ASP SEQRES 47 A 687 ALA PHE LYS GLU CYS PHE VAL SER ARG PRO HIS PRO LYS SEQRES 48 A 687 PRO LYS GLN PHE SER SER PHE GLU LYS ARG ALA LYS ILE SEQRES 49 A 687 PHE CYS ALA ARG GLN ASN CYS SER HIS ASP TRP GLY ILE SEQRES 50 A 687 HIS VAL LYS TYR LYS THR PHE GLU ILE PRO VAL ILE LYS SEQRES 51 A 687 ILE GLU SER PHE VAL VAL GLU ASP ILE ALA THR GLY VAL SEQRES 52 A 687 GLN THR LEU TYR SER LYS TRP LYS ASP PHE HIS PHE GLU SEQRES 53 A 687 LYS ILE PRO PHE ASP PRO ALA GLU MET SER LYS SEQRES 1 C 20 GTP G C G C G G C U U C G G SEQRES 2 C 20 C C G C G C C MODRES 4AY2 GTP C 1 G GUANOSINE-5'-TRIPHOSPHATE HET GTP C 1 32 HET ZN A1923 1 HET ADP A1924 27 HET MG A1925 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 ZN ZN 2+ FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 MG MG 2+ FORMUL 6 HOH *70(H2 O) HELIX 1 1 ARG A 244 ALA A 251 1 8 HELIX 2 2 ALA A 251 LYS A 256 1 6 HELIX 3 3 GLY A 269 LYS A 284 1 16 HELIX 4 4 GLN A 299 PHE A 314 1 16 HELIX 5 5 PRO A 333 ASN A 340 1 8 HELIX 6 6 THR A 347 LYS A 357 1 11 HELIX 7 7 SER A 362 PHE A 366 5 5 HELIX 8 8 CYS A 374 THR A 377 5 4 HELIX 9 9 HIS A 381 GLY A 396 1 16 HELIX 10 10 ASN A 419 ASP A 435 1 17 HELIX 11 11 ASN A 445 VAL A 452 1 8 HELIX 12 12 LYS A 470 CYS A 490 1 21 HELIX 13 13 ASP A 492 LEU A 496 5 5 HELIX 14 14 THR A 506 CYS A 520 1 15 HELIX 15 15 GLU A 530 ALA A 558 1 29 HELIX 16 16 ARG A 559 ARG A 575 1 17 HELIX 17 17 ASP A 580 ARG A 602 1 23 HELIX 18 18 ASP A 603 GLU A 607 5 5 HELIX 19 19 ASN A 608 ASN A 625 1 18 HELIX 20 20 THR A 636 GLY A 649 1 14 HELIX 21 21 ASN A 650 SER A 654 5 5 HELIX 22 22 ASN A 744 GLN A 769 1 26 HELIX 23 23 ASP A 772 GLN A 794 1 23 HELIX 24 24 GLY A 835 LYS A 839 5 5 HELIX 25 25 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 ILE A 660 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 ALA A 817 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 THR A 903 -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 PHE A 856 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 2.04 LINK O3' GTP C 1 P G C 2 1555 1555 1.74 LINK SG CYS A 810 ZN ZN A1923 1555 1555 2.28 LINK SG CYS A 813 ZN ZN A1923 1555 1555 2.16 LINK SG CYS A 864 ZN ZN A1923 1555 1555 2.29 LINK SG CYS A 869 ZN ZN A1923 1555 1555 2.58 LINK O1B ADP A1924 MG MG A1925 1555 1555 2.62 CISPEP 1 ALA A 329 GLU A 330 0 -4.52 CISPEP 2 SER A 399 GLY A 400 0 -9.92 CISPEP 3 GLY A 578 PHE A 579 0 -0.26 CISPEP 4 GLY A 689 ASP A 690 0 -5.32 CISPEP 5 LYS A 796 PRO A 797 0 -12.40 SITE 1 AC1 4 CYS A 810 CYS A 813 CYS A 864 CYS A 869 SITE 1 AC2 10 LYS A 242 ARG A 244 GLN A 247 THR A 266 SITE 2 AC2 10 GLY A 267 CYS A 268 GLY A 269 LYS A 270 SITE 3 AC2 10 THR A 271 MG A1925 SITE 1 AC3 3 THR A 271 ASP A 372 ADP A1924 CRYST1 47.745 76.156 221.222 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 0.020945 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004520 0.00000