HEADER HYDROLASE 27-MAY-11 2YKG 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 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3'; COMPND 10 CHAIN: C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_TAXID: 9606 KEYWDS HYDROLASE, INNATE IMMUNITY EXPDTA X-RAY DIFFRACTION AUTHOR D.LUO,A.M.PYLE REVDAT 1 26-OCT-11 2YKG 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 93.72 REMARK 3 NUMBER OF REFLECTIONS : 25452 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) : 0.22300 REMARK 3 R VALUE (WORKING SET) : 0.22036 REMARK 3 FREE R VALUE : 0.27310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1341 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) : 2.500 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.565 REMARK 3 REFLECTION IN BIN (WORKING SET) : 649 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 33.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.363 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.489 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4995 REMARK 3 NUCLEIC ACID ATOMS : 424 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.853 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77 REMARK 3 B22 (A**2) : 1.53 REMARK 3 B33 (A**2) : -2.30 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.732 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.331 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.258 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.128 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5567 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7622 ; 1.339 ; 2.058 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 631 ; 6.255 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 220 ;38.537 ;24.591 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 898 ;18.123 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;14.911 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 879 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3987 ; 0.005 ; 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): 3180 ; 0.533 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5119 ; 1.012 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2387 ; 1.331 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2503 ; 2.168 ; 4.500 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 236 A 455 REMARK 3 ORIGIN FOR THE GROUP (A): -9.1380 13.4627 -16.5538 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.2092 REMARK 3 T33: 0.2283 T12: 0.0032 REMARK 3 T13: -0.0091 T23: -0.0693 REMARK 3 L TENSOR REMARK 3 L11: 1.4922 L22: 1.5235 REMARK 3 L33: 1.9907 L12: -0.0862 REMARK 3 L13: -0.7417 L23: 0.4108 REMARK 3 S TENSOR REMARK 3 S11: -0.0390 S12: 0.1542 S13: 0.0044 REMARK 3 S21: -0.0749 S22: 0.0387 S23: 0.0425 REMARK 3 S31: -0.0093 S32: -0.1045 S33: 0.0003 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 795 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9997 -18.9750 -22.5688 REMARK 3 T TENSOR REMARK 3 T11: 0.2637 T22: 0.3276 REMARK 3 T33: 0.2743 T12: 0.0747 REMARK 3 T13: 0.0129 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 0.2382 L22: 1.6549 REMARK 3 L33: 0.7779 L12: -0.3544 REMARK 3 L13: -0.3258 L23: 0.7287 REMARK 3 S TENSOR REMARK 3 S11: -0.0630 S12: -0.0788 S13: 0.0004 REMARK 3 S21: 0.0874 S22: -0.0685 S23: -0.0240 REMARK 3 S31: 0.2240 S32: 0.0076 S33: 0.1315 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 796 A 922 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6991 7.4075 -49.8311 REMARK 3 T TENSOR REMARK 3 T11: 0.1625 T22: 0.1840 REMARK 3 T33: 0.0526 T12: -0.0076 REMARK 3 T13: 0.0608 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 7.3239 L22: 3.1027 REMARK 3 L33: 9.2821 L12: 0.3868 REMARK 3 L13: -2.5728 L23: -0.5064 REMARK 3 S TENSOR REMARK 3 S11: -0.1677 S12: -0.0122 S13: -0.2034 REMARK 3 S21: -0.3508 S22: -0.2045 S23: 0.0095 REMARK 3 S31: 0.0567 S32: 0.0242 S33: 0.3722 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 10 REMARK 3 RESIDUE RANGE : D 1 D 10 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5071 1.1625 -29.4493 REMARK 3 T TENSOR REMARK 3 T11: 0.2125 T22: 0.5045 REMARK 3 T33: 0.4139 T12: -0.0629 REMARK 3 T13: -0.0883 T23: -0.1884 REMARK 3 L TENSOR REMARK 3 L11: 10.2871 L22: 9.5764 REMARK 3 L33: 4.7037 L12: -7.4719 REMARK 3 L13: -3.7610 L23: 7.7275 REMARK 3 S TENSOR REMARK 3 S11: 0.1537 S12: -0.1407 S13: -0.5485 REMARK 3 S21: 0.5565 S22: 0.8979 S23: -0.4259 REMARK 3 S31: -0.0588 S32: 0.7555 S33: -1.0516 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN REMARK 3 THE RIDING POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 2YKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-11. REMARK 100 THE PDBE ID CODE IS EBI-48455. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 173 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 : 26861 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.50 REMARK 200 RESOLUTION RANGE LOW (A) : 45.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 5 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.50 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.6 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.3 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.5 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 PRO A 240 REMARK 465 PHE A 241 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 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 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 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 LYS A 242 CG CD CE NZ REMARK 470 THR A 260 CG2 REMARK 470 GLN A 287 CG CD OE1 NE2 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 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 PHE A 579 CG CD1 CD2 CE1 CE2 CZ 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 ASP A 690 CG OD1 OD2 REMARK 470 HIS A 691 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 701 CG OD1 OD2 REMARK 470 GLU A 702 CG CD OE1 OE2 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 GLU A 795 CB CG CD OE1 OE2 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 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 LYS A 807 NZ REMARK 480 LYS A 878 NZ REMARK 480 GLU A 914 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 SG CYS A 263 O HOH A 2007 2.00 REMARK 500 O HOH A 2076 O HOH A 2077 2.15 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 LYS A 807 CE LYS A 807 NZ -0.987 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 LYS A 807 CD - CE - NZ ANGL. DEV. = 51.1 DEGREES REMARK 500 C C 10 O4' - C1' - N1 ANGL. DEV. = 5.3 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 LEU A 237 30.16 -85.45 REMARK 500 ARG A 316 -42.71 96.31 REMARK 500 LYS A 379 -130.13 55.63 REMARK 500 SER A 398 79.11 -154.46 REMARK 500 ASP A 416 46.39 -82.95 REMARK 500 CYS A 520 62.93 -163.34 REMARK 500 ALA A 558 -154.01 -111.57 REMARK 500 ALA A 577 55.69 -170.86 REMARK 500 ASP A 580 -171.02 -65.97 REMARK 500 PHE A 655 -53.28 101.62 REMARK 500 HIS A 691 168.16 161.42 REMARK 500 ASN A 692 50.17 -99.08 REMARK 500 VAL A 699 -61.25 -99.89 REMARK 500 GLU A 702 105.65 -174.52 REMARK 500 ILE A 722 79.24 -150.85 REMARK 500 LYS A 723 79.87 -115.18 REMARK 500 GLN A 794 23.63 -78.57 REMARK 500 LYS A 803 -27.60 68.05 REMARK 500 LYS A 814 -2.36 91.09 REMARK 500 CYS A 818 -172.29 -170.76 REMARK 500 ASP A 828 -44.67 76.31 REMARK 500 ASN A 868 54.94 -112.95 REMARK 500 CYS A 869 -67.89 -157.43 REMARK 500 THR A 881 -3.43 69.80 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 THR A 482 24.6 L L OUTSIDE RANGE REMARK 500 SER A 654 21.5 L L OUTSIDE RANGE 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 864 SG 106.6 REMARK 620 3 CYS A 869 SG 102.1 118.8 REMARK 620 4 CYS A 810 SG 107.0 118.1 102.6 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 DBREF 2YKG A 230 925 UNP O95786 DDX58_HUMAN 230 925 DBREF 2YKG C 1 10 PDB 2YKG 2YKG 1 10 DBREF 2YKG D 1 10 PDB 2YKG 2YKG 1 10 SEQADV 2YKG ASN A 306 UNP O95786 GLN 306 CONFLICT SEQADV 2YKG THR A 419 UNP O95786 ASN 419 CONFLICT SEQADV 2YKG ASP A 828 UNP O95786 GLU 828 CONFLICT SEQRES 1 A 696 SER GLU VAL SER ASP THR ASN LEU TYR SER PRO PHE LYS SEQRES 2 A 696 PRO ARG ASN TYR GLN LEU GLU LEU ALA LEU PRO ALA MET SEQRES 3 A 696 LYS GLY LYS ASN THR ILE ILE CYS ALA PRO THR GLY CYS SEQRES 4 A 696 GLY LYS THR PHE VAL SER LEU LEU ILE CYS GLU HIS HIS SEQRES 5 A 696 LEU LYS LYS PHE PRO GLN GLY GLN LYS GLY LYS VAL VAL SEQRES 6 A 696 PHE PHE ALA ASN GLN ILE PRO VAL TYR GLU GLN ASN LYS SEQRES 7 A 696 SER VAL PHE SER LYS TYR PHE GLU ARG HIS GLY TYR ARG SEQRES 8 A 696 VAL THR GLY ILE SER GLY ALA THR ALA GLU ASN VAL PRO SEQRES 9 A 696 VAL GLU GLN ILE VAL GLU ASN ASN ASP ILE ILE ILE LEU SEQRES 10 A 696 THR PRO GLN ILE LEU VAL ASN ASN LEU LYS LYS GLY THR SEQRES 11 A 696 ILE PRO SER LEU SER ILE PHE THR LEU MET ILE PHE ASP SEQRES 12 A 696 GLU CYS HIS ASN THR SER LYS GLN HIS PRO TYR ASN MET SEQRES 13 A 696 ILE MET PHE ASN TYR LEU ASP GLN LYS LEU GLY GLY SER SEQRES 14 A 696 SER GLY PRO LEU PRO GLN VAL ILE GLY LEU THR ALA SER SEQRES 15 A 696 VAL GLY VAL GLY ASP ALA LYS THR THR ASP GLU ALA LEU SEQRES 16 A 696 ASP TYR ILE CYS LYS LEU CYS ALA SER LEU ASP ALA SER SEQRES 17 A 696 VAL ILE ALA THR VAL LYS HIS ASN LEU GLU GLU LEU GLU SEQRES 18 A 696 GLN VAL VAL TYR LYS PRO GLN LYS PHE PHE ARG LYS VAL SEQRES 19 A 696 GLU SER ARG ILE SER ASP LYS PHE LYS TYR ILE ILE ALA SEQRES 20 A 696 GLN LEU MET ARG ASP THR GLU SER LEU ALA LYS ARG ILE SEQRES 21 A 696 CYS LYS ASP LEU GLU ASN LEU SER GLN ILE GLN ASN ARG SEQRES 22 A 696 GLU PHE GLY THR GLN LYS TYR GLU GLN TRP ILE VAL THR SEQRES 23 A 696 VAL GLN LYS ALA CYS MET VAL PHE GLN MET PRO ASP LYS SEQRES 24 A 696 ASP GLU GLU SER ARG ILE CYS LYS ALA LEU PHE LEU TYR SEQRES 25 A 696 THR SER HIS LEU ARG LYS TYR ASN ASP ALA LEU ILE ILE SEQRES 26 A 696 SER GLU HIS ALA ARG MET LYS ASP ALA LEU ASP TYR LEU SEQRES 27 A 696 LYS ASP PHE PHE SER ASN VAL ARG ALA ALA GLY PHE ASP SEQRES 28 A 696 GLU ILE GLU GLN ASP LEU THR GLN ARG PHE GLU GLU LYS SEQRES 29 A 696 LEU GLN GLU LEU GLU SER VAL SER ARG ASP PRO SER ASN SEQRES 30 A 696 GLU ASN PRO LYS LEU GLU ASP LEU CYS PHE ILE LEU GLN SEQRES 31 A 696 GLU GLU TYR HIS LEU ASN PRO GLU THR ILE THR ILE LEU SEQRES 32 A 696 PHE VAL LYS THR ARG ALA LEU VAL ASP ALA LEU LYS ASN SEQRES 33 A 696 TRP ILE GLU GLY ASN PRO LYS LEU SER PHE LEU LYS PRO SEQRES 34 A 696 GLY ILE LEU THR GLY ARG GLY LYS THR ASN GLN ASN THR SEQRES 35 A 696 GLY MET THR LEU PRO ALA GLN LYS CYS ILE LEU ASP ALA SEQRES 36 A 696 PHE LYS ALA SER GLY ASP HIS ASN ILE LEU ILE ALA THR SEQRES 37 A 696 SER VAL ALA ASP GLU GLY ILE ASP ILE ALA GLN CYS ASN SEQRES 38 A 696 LEU VAL ILE LEU TYR GLU TYR VAL GLY ASN VAL ILE LYS SEQRES 39 A 696 MET ILE GLN THR ARG GLY ARG GLY ARG ALA ARG GLY SER SEQRES 40 A 696 LYS CYS PHE LEU LEU THR SER ASN ALA GLY VAL ILE GLU SEQRES 41 A 696 LYS GLU GLN ILE ASN MET TYR LYS GLU LYS MET MET ASN SEQRES 42 A 696 ASP SER ILE LEU ARG LEU GLN THR TRP ASP GLU ALA VAL SEQRES 43 A 696 PHE ARG GLU LYS ILE LEU HIS ILE GLN THR HIS GLU LYS SEQRES 44 A 696 PHE ILE ARG ASP SER GLN GLU LYS PRO LYS PRO VAL PRO SEQRES 45 A 696 ASP LYS GLU ASN LYS LYS LEU LEU CYS ARG LYS CYS LYS SEQRES 46 A 696 ALA LEU ALA CYS TYR THR ALA ASP VAL ARG VAL ILE GLU SEQRES 47 A 696 ASP CYS HIS TYR THR VAL LEU GLY ASP ALA PHE LYS GLU SEQRES 48 A 696 CYS PHE VAL SER ARG PRO HIS PRO LYS PRO LYS GLN PHE SEQRES 49 A 696 SER SER PHE GLU LYS ARG ALA LYS ILE PHE CYS ALA ARG SEQRES 50 A 696 GLN ASN CYS SER HIS ASP TRP GLY ILE HIS VAL LYS TYR SEQRES 51 A 696 LYS THR PHE GLU ILE PRO VAL ILE LYS ILE GLU SER PHE SEQRES 52 A 696 VAL VAL GLU ASP ILE ALA THR GLY VAL GLN THR LEU TYR SEQRES 53 A 696 SER LYS TRP LYS ASP PHE HIS PHE GLU LYS ILE PRO PHE SEQRES 54 A 696 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 ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 4 ZN ZN 2+ FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *99(H2 O) HELIX 1 1 ARG A 244 LYS A 256 1 13 HELIX 2 2 GLY A 269 PHE A 285 1 17 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 VAL A 453 1 9 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 576 1 18 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 PRO A 604 GLU A 607 5 4 HELIX 19 19 ASN A 608 HIS A 623 1 16 HELIX 20 20 THR A 636 ASN A 650 1 15 HELIX 21 21 ASN A 744 GLN A 769 1 26 HELIX 22 22 ASP A 772 GLN A 794 1 23 HELIX 23 23 ALA A 837 GLU A 840 5 4 HELIX 24 24 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 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 2 VAL A 823 ILE A 826 0 SHEET 2 AD 2 HIS A 830 VAL A 833 -1 O HIS A 830 N ILE A 826 SHEET 1 AE 4 PHE A 842 GLN A 852 0 SHEET 2 AE 4 GLU A 857 CYS A 864 -1 O LYS A 858 N LYS A 851 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 2.05 LINK ZN ZN A 927 SG CYS A 813 1555 1555 2.23 LINK ZN ZN A 927 SG CYS A 864 1555 1555 2.38 LINK ZN ZN A 927 SG CYS A 869 1555 1555 2.48 LINK ZN ZN A 927 SG CYS A 810 1555 1555 2.44 CISPEP 1 ALA A 329 GLU A 330 0 1.64 CISPEP 2 SER A 399 GLY A 400 0 -19.13 CISPEP 3 GLY A 413 VAL A 414 0 -3.68 CISPEP 4 GLY A 578 PHE A 579 0 -7.11 CISPEP 5 SER A 654 PHE A 655 0 11.28 CISPEP 6 ASP A 690 HIS A 691 0 -2.51 SITE 1 AC1 4 CYS A 810 CYS A 813 CYS A 864 CYS A 869 SITE 1 AC2 8 PRO A 265 THR A 266 GLY A 267 CYS A 268 SITE 2 AC2 8 GLY A 269 LYS A 270 THR A 271 HOH A2028 CRYST1 47.618 76.208 219.825 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 0.021000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004549 0.00000