HEADER ANTIVIRAL PROTEIN 05-JUN-18 6GPG TITLE STRUCTURE OF THE RIG-I SINGLETON-MERTEN SYNDROME VARIANT C268F COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*UP*CP*G)-3'); COMPND 3 CHAIN: B, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROBABLE ATP-DEPENDENT RNA HELICASE DDX58; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: DEAD BOX PROTEIN 58,RIG-I-LIKE RECEPTOR 1,RLR-1,RETINOIC COMPND 9 ACID-INDUCIBLE GENE 1 PROTEIN,RIG-1,RETINOIC ACID-INDUCIBLE GENE I COMPND 10 PROTEIN,RIG-I; COMPND 11 EC: 3.6.4.13; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: DDX58; SOURCE 10 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 11 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS INNATE IMMUNE SYSTEM, RIG-I, SINGLETON-MERTEN SYNDROME, RNA-DEPENDENT KEYWDS 2 ATPASE, RNA BINDING PROTEIN, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.LAESSIG,K.LAMMENS,K.-P.HOPFNER REVDAT 2 15-MAY-24 6GPG 1 AUTHOR REVDAT 1 08-AUG-18 6GPG 0 JRNL AUTH C.LASSIG,K.LAMMENS,J.L.GORENFLOS LOPEZ,S.MICHALSKI, JRNL AUTH 2 O.FETTSCHER,K.P.HOPFNER JRNL TITL UNIFIED MECHANISMS FOR SELF-RNA RECOGNITION BY RIG-I JRNL TITL 2 SINGLETON-MERTEN SYNDROME VARIANTS. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 30047865 JRNL DOI 10.7554/ELIFE.38958 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 22649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1110 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 46.4742 - 5.7848 1.00 2884 159 0.1872 0.2184 REMARK 3 2 5.7848 - 4.5929 1.00 2761 106 0.2023 0.2398 REMARK 3 3 4.5929 - 4.0127 1.00 2695 135 0.1876 0.2500 REMARK 3 4 4.0127 - 3.6460 1.00 2651 160 0.2121 0.2975 REMARK 3 5 3.6460 - 3.3847 1.00 2665 140 0.2449 0.3512 REMARK 3 6 3.3847 - 3.1852 1.00 2637 147 0.2813 0.3445 REMARK 3 7 3.1852 - 3.0257 1.00 2658 121 0.3170 0.3596 REMARK 3 8 3.0257 - 2.8940 0.98 2588 142 0.3426 0.4077 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 5988 REMARK 3 ANGLE : 1.238 8198 REMARK 3 CHIRALITY : 0.062 930 REMARK 3 PLANARITY : 0.007 954 REMARK 3 DIHEDRAL : 9.388 3590 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'B' ) REMARK 3 ORIGIN FOR THE GROUP (A): -92.1805 92.8558 -7.7354 REMARK 3 T TENSOR REMARK 3 T11: 0.8270 T22: 1.8022 REMARK 3 T33: 1.3146 T12: -0.0642 REMARK 3 T13: -0.1530 T23: 0.4356 REMARK 3 L TENSOR REMARK 3 L11: 1.8463 L22: 2.7663 REMARK 3 L33: 2.7340 L12: -0.1173 REMARK 3 L13: 1.1119 L23: 0.3031 REMARK 3 S TENSOR REMARK 3 S11: -0.2858 S12: 0.0471 S13: 0.7504 REMARK 3 S21: -0.0718 S22: -0.0626 S23: -1.1794 REMARK 3 S31: -0.4525 S32: 2.0751 S33: 0.5778 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'C' ) REMARK 3 ORIGIN FOR THE GROUP (A): -94.1389 90.4847 -5.0042 REMARK 3 T TENSOR REMARK 3 T11: 0.8417 T22: 1.6975 REMARK 3 T33: 1.0498 T12: -0.0400 REMARK 3 T13: -0.2381 T23: 0.0677 REMARK 3 L TENSOR REMARK 3 L11: 2.0002 L22: 1.9616 REMARK 3 L33: 1.4548 L12: -0.0515 REMARK 3 L13: 1.3914 L23: -0.4754 REMARK 3 S TENSOR REMARK 3 S11: 0.0607 S12: 0.3057 S13: 0.5806 REMARK 3 S21: 0.0420 S22: 0.4103 S23: 0.4925 REMARK 3 S31: -0.0341 S32: 1.1428 S33: 0.5217 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'I' ) REMARK 3 ORIGIN FOR THE GROUP (A):-100.0604 87.8819 -0.5778 REMARK 3 T TENSOR REMARK 3 T11: 0.7061 T22: 1.2643 REMARK 3 T33: 0.8867 T12: 0.1100 REMARK 3 T13: -0.1085 T23: 0.1339 REMARK 3 L TENSOR REMARK 3 L11: 1.8414 L22: 1.5123 REMARK 3 L33: 2.3802 L12: -0.2209 REMARK 3 L13: 0.6356 L23: -0.1159 REMARK 3 S TENSOR REMARK 3 S11: -0.2243 S12: -0.1066 S13: 0.4517 REMARK 3 S21: 0.0734 S22: -0.1849 S23: -0.5205 REMARK 3 S31: -0.3084 S32: 0.8355 S33: 0.3487 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 6GPG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22649 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.894 REMARK 200 RESOLUTION RANGE LOW (A) : 46.468 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.09 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MOPS PH 7.5, 17.5 % (W/V) PEG REMARK 280 3350, 0.25 M NASCN, 3 % (V/V) 2,2,2 TRIFLUOROETHANOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.02000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.51000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.76500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.25500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.27500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.02000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 36.51000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 18.25500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 54.76500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 91.27500 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: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, A 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 G B 14 REMARK 465 C C 1 REMARK 465 MET A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 HIS A 217 REMARK 465 HIS A 218 REMARK 465 SER A 219 REMARK 465 SER A 220 REMARK 465 GLY A 221 REMARK 465 LEU A 222 REMARK 465 GLU A 223 REMARK 465 VAL A 224 REMARK 465 LEU A 225 REMARK 465 PHE A 226 REMARK 465 GLN A 227 REMARK 465 GLY A 228 REMARK 465 PRO A 229 REMARK 465 HIS A 230 REMARK 465 MET A 231 REMARK 465 VAL A 232 REMARK 465 SER A 233 REMARK 465 ASP A 234 REMARK 465 THR A 235 REMARK 465 ASN A 236 REMARK 465 LEU A 237 REMARK 465 TYR A 238 REMARK 465 GLU A 494 REMARK 465 ASN A 495 REMARK 465 LEU A 496 REMARK 465 SER A 497 REMARK 465 GLN A 498 REMARK 465 ILE A 499 REMARK 465 GLN A 500 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 MET A 923 REMARK 465 SER A 924 REMARK 465 LYS A 925 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 CG HIS A 847 NZ LYS A 858 1.98 REMARK 500 O ALA A 774 OE1 GLU A 778 1.98 REMARK 500 NZ LYS A 536 O ARG A 811 2.14 REMARK 500 CD2 HIS A 847 NZ LYS A 858 2.14 REMARK 500 NE2 HIS A 375 OD2 ASP A 701 2.15 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 CYS A 535 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 LEU A 567 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 ASP A 705 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 859 NE - CZ - NH1 ANGL. DEV. = 3.3 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 PRO A 240 46.37 -89.93 REMARK 500 LYS A 242 68.21 60.35 REMARK 500 LYS A 379 -75.31 -38.13 REMARK 500 LYS A 491 19.71 51.86 REMARK 500 THR A 506 -157.29 -96.03 REMARK 500 THR A 697 -62.16 -95.30 REMARK 500 SER A 698 140.06 -170.77 REMARK 500 GLU A 702 -54.65 -26.52 REMARK 500 ASP A 705 132.22 -28.34 REMARK 500 LYS A 814 19.41 57.25 REMARK 500 CYS A 818 -172.94 -172.66 REMARK 500 GLU A 828 -1.57 67.33 REMARK 500 THR A 832 -168.41 -103.43 REMARK 500 PRO A 850 75.51 -69.90 REMARK 500 SER A 870 44.56 39.80 REMARK 500 LYS A 880 -64.31 -26.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 346 THR A 347 147.77 REMARK 500 SER A 378 LYS A 379 -144.03 REMARK 500 GLN A 507 LYS A 508 148.99 REMARK 500 ASP A 701 GLU A 702 -138.87 REMARK 500 PHE A 853 SER A 854 -127.34 REMARK 500 TYR A 879 LYS A 880 -142.63 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 810 SG REMARK 620 2 CYS A 813 SG 99.2 REMARK 620 3 CYS A 864 SG 162.0 92.3 REMARK 620 4 CYS A 869 SG 109.8 108.4 79.1 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1002 DBREF 6GPG B 1 14 PDB 6GPG 6GPG 1 14 DBREF 6GPG C 1 14 PDB 6GPG 6GPG 1 14 DBREF 6GPG A 232 925 UNP O95786 DDX58_HUMAN 232 925 SEQADV 6GPG MET A 212 UNP O95786 INITIATING METHIONINE SEQADV 6GPG HIS A 213 UNP O95786 EXPRESSION TAG SEQADV 6GPG HIS A 214 UNP O95786 EXPRESSION TAG SEQADV 6GPG HIS A 215 UNP O95786 EXPRESSION TAG SEQADV 6GPG HIS A 216 UNP O95786 EXPRESSION TAG SEQADV 6GPG HIS A 217 UNP O95786 EXPRESSION TAG SEQADV 6GPG HIS A 218 UNP O95786 EXPRESSION TAG SEQADV 6GPG SER A 219 UNP O95786 EXPRESSION TAG SEQADV 6GPG SER A 220 UNP O95786 EXPRESSION TAG SEQADV 6GPG GLY A 221 UNP O95786 EXPRESSION TAG SEQADV 6GPG LEU A 222 UNP O95786 EXPRESSION TAG SEQADV 6GPG GLU A 223 UNP O95786 EXPRESSION TAG SEQADV 6GPG VAL A 224 UNP O95786 EXPRESSION TAG SEQADV 6GPG LEU A 225 UNP O95786 EXPRESSION TAG SEQADV 6GPG PHE A 226 UNP O95786 EXPRESSION TAG SEQADV 6GPG GLN A 227 UNP O95786 EXPRESSION TAG SEQADV 6GPG GLY A 228 UNP O95786 EXPRESSION TAG SEQADV 6GPG PRO A 229 UNP O95786 EXPRESSION TAG SEQADV 6GPG HIS A 230 UNP O95786 EXPRESSION TAG SEQADV 6GPG MET A 231 UNP O95786 EXPRESSION TAG SEQADV 6GPG PHE A 268 UNP O95786 CYS 268 ENGINEERED MUTATION SEQRES 1 B 14 C G A C G C U A G C G U C SEQRES 2 B 14 G SEQRES 1 C 14 C G A C G C U A G C G U C SEQRES 2 C 14 G SEQRES 1 A 714 MET HIS HIS HIS HIS HIS HIS SER SER GLY LEU GLU VAL SEQRES 2 A 714 LEU PHE GLN GLY PRO HIS MET VAL SER ASP THR ASN LEU SEQRES 3 A 714 TYR SER PRO PHE LYS PRO ARG ASN TYR GLN LEU GLU LEU SEQRES 4 A 714 ALA LEU PRO ALA MET LYS GLY LYS ASN THR ILE ILE CYS SEQRES 5 A 714 ALA PRO THR GLY PHE GLY LYS THR PHE VAL SER LEU LEU SEQRES 6 A 714 ILE CYS GLU HIS HIS LEU LYS LYS PHE PRO GLN GLY GLN SEQRES 7 A 714 LYS GLY LYS VAL VAL PHE PHE ALA ASN GLN ILE PRO VAL SEQRES 8 A 714 TYR GLU GLN GLN LYS SER VAL PHE SER LYS TYR PHE GLU SEQRES 9 A 714 ARG HIS GLY TYR ARG VAL THR GLY ILE SER GLY ALA THR SEQRES 10 A 714 ALA GLU ASN VAL PRO VAL GLU GLN ILE VAL GLU ASN ASN SEQRES 11 A 714 ASP ILE ILE ILE LEU THR PRO GLN ILE LEU VAL ASN ASN SEQRES 12 A 714 LEU LYS LYS GLY THR ILE PRO SER LEU SER ILE PHE THR SEQRES 13 A 714 LEU MET ILE PHE ASP GLU CYS HIS ASN THR SER LYS GLN SEQRES 14 A 714 HIS PRO TYR ASN MET ILE MET PHE ASN TYR LEU ASP GLN SEQRES 15 A 714 LYS LEU GLY GLY SER SER GLY PRO LEU PRO GLN VAL ILE SEQRES 16 A 714 GLY LEU THR ALA SER VAL GLY VAL GLY ASP ALA LYS ASN SEQRES 17 A 714 THR ASP GLU ALA LEU ASP TYR ILE CYS LYS LEU CYS ALA SEQRES 18 A 714 SER LEU ASP ALA SER VAL ILE ALA THR VAL LYS HIS ASN SEQRES 19 A 714 LEU GLU GLU LEU GLU GLN VAL VAL TYR LYS PRO GLN LYS SEQRES 20 A 714 PHE PHE ARG LYS VAL GLU SER ARG ILE SER ASP LYS PHE SEQRES 21 A 714 LYS TYR ILE ILE ALA GLN LEU MET ARG ASP THR GLU SER SEQRES 22 A 714 LEU ALA LYS ARG ILE CYS LYS ASP LEU GLU ASN LEU SER SEQRES 23 A 714 GLN ILE GLN ASN ARG GLU PHE GLY THR GLN LYS TYR GLU SEQRES 24 A 714 GLN TRP ILE VAL THR VAL GLN LYS ALA CYS MET VAL PHE SEQRES 25 A 714 GLN MET PRO ASP LYS ASP GLU GLU SER ARG ILE CYS LYS SEQRES 26 A 714 ALA LEU PHE LEU TYR THR SER HIS LEU ARG LYS TYR ASN SEQRES 27 A 714 ASP ALA LEU ILE ILE SER GLU HIS ALA ARG MET LYS ASP SEQRES 28 A 714 ALA LEU ASP TYR LEU LYS ASP PHE PHE SER ASN VAL ARG SEQRES 29 A 714 ALA ALA GLY PHE ASP GLU ILE GLU GLN ASP LEU THR GLN SEQRES 30 A 714 ARG PHE GLU GLU LYS LEU GLN GLU LEU GLU SER VAL SER SEQRES 31 A 714 ARG ASP PRO SER ASN GLU ASN PRO LYS LEU GLU ASP LEU SEQRES 32 A 714 CYS PHE ILE LEU GLN GLU GLU TYR HIS LEU ASN PRO GLU SEQRES 33 A 714 THR ILE THR ILE LEU PHE VAL LYS THR ARG ALA LEU VAL SEQRES 34 A 714 ASP ALA LEU LYS ASN TRP ILE GLU GLY ASN PRO LYS LEU SEQRES 35 A 714 SER PHE LEU LYS PRO GLY ILE LEU THR GLY ARG GLY LYS SEQRES 36 A 714 THR ASN GLN ASN THR GLY MET THR LEU PRO ALA GLN LYS SEQRES 37 A 714 CYS ILE LEU ASP ALA PHE LYS ALA SER GLY ASP HIS ASN SEQRES 38 A 714 ILE LEU ILE ALA THR SER VAL ALA ASP GLU GLY ILE ASP SEQRES 39 A 714 ILE ALA GLN CYS ASN LEU VAL ILE LEU TYR GLU TYR VAL SEQRES 40 A 714 GLY ASN VAL ILE LYS MET ILE GLN THR ARG GLY ARG GLY SEQRES 41 A 714 ARG ALA ARG GLY SER LYS CYS PHE LEU LEU THR SER ASN SEQRES 42 A 714 ALA GLY VAL ILE GLU LYS GLU GLN ILE ASN MET TYR LYS SEQRES 43 A 714 GLU LYS MET MET ASN ASP SER ILE LEU ARG LEU GLN THR SEQRES 44 A 714 TRP ASP GLU ALA VAL PHE ARG GLU LYS ILE LEU HIS ILE SEQRES 45 A 714 GLN THR HIS GLU LYS PHE ILE ARG ASP SER GLN GLU LYS SEQRES 46 A 714 PRO LYS PRO VAL PRO ASP LYS GLU ASN LYS LYS LEU LEU SEQRES 47 A 714 CYS ARG LYS CYS LYS ALA LEU ALA CYS TYR THR ALA ASP SEQRES 48 A 714 VAL ARG VAL ILE GLU GLU CYS HIS TYR THR VAL LEU GLY SEQRES 49 A 714 ASP ALA PHE LYS GLU CYS PHE VAL SER ARG PRO HIS PRO SEQRES 50 A 714 LYS PRO LYS GLN PHE SER SER PHE GLU LYS ARG ALA LYS SEQRES 51 A 714 ILE PHE CYS ALA ARG GLN ASN CYS SER HIS ASP TRP GLY SEQRES 52 A 714 ILE HIS VAL LYS TYR LYS THR PHE GLU ILE PRO VAL ILE SEQRES 53 A 714 LYS ILE GLU SER PHE VAL VAL GLU ASP ILE ALA THR GLY SEQRES 54 A 714 VAL GLN THR LEU TYR SER LYS TRP LYS ASP PHE HIS PHE SEQRES 55 A 714 GLU LYS ILE PRO PHE ASP PRO ALA GLU MET SER LYS HET ZN A1001 1 HET MG A1002 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 4 ZN ZN 2+ FORMUL 5 MG MG 2+ HELIX 1 AA1 ARG A 244 LYS A 256 1 13 HELIX 2 AA2 GLY A 269 LYS A 284 1 16 HELIX 3 AA3 GLN A 299 GLU A 315 1 17 HELIX 4 AA4 ARG A 316 GLY A 318 5 3 HELIX 5 AA5 SER A 325 ALA A 329 5 5 HELIX 6 AA6 PRO A 333 ASN A 340 1 8 HELIX 7 AA7 THR A 347 LYS A 357 1 11 HELIX 8 AA8 SER A 362 PHE A 366 5 5 HELIX 9 AA9 CYS A 374 THR A 377 5 4 HELIX 10 AB1 HIS A 381 GLY A 396 1 16 HELIX 11 AB2 ASN A 419 LEU A 434 1 16 HELIX 12 AB3 ASN A 445 GLU A 450 1 6 HELIX 13 AB4 ASP A 469 CYS A 490 1 22 HELIX 14 AB5 GLN A 507 MET A 521 1 15 HELIX 15 AB6 LYS A 528 ALA A 558 1 31 HELIX 16 AB7 ARG A 559 ALA A 576 1 18 HELIX 17 AB8 ASP A 580 ARG A 602 1 23 HELIX 18 AB9 ASN A 608 ASN A 625 1 18 HELIX 19 AC1 THR A 636 ASN A 650 1 15 HELIX 20 AC2 PRO A 651 SER A 654 5 4 HELIX 21 AC3 ASN A 720 ARG A 728 1 9 HELIX 22 AC4 GLY A 729 ARG A 732 5 4 HELIX 23 AC5 ASN A 744 THR A 770 1 27 HELIX 24 AC6 ASP A 772 GLU A 795 1 24 HELIX 25 AC7 ALA A 821 VAL A 823 5 3 HELIX 26 AC8 GLY A 835 CYS A 841 1 7 SHEET 1 AA1 7 VAL A 321 ILE A 324 0 SHEET 2 AA1 7 ILE A 343 LEU A 346 1 O ILE A 345 N THR A 322 SHEET 3 AA1 7 VAL A 293 PHE A 296 1 N PHE A 295 O LEU A 346 SHEET 4 AA1 7 LEU A 368 ASP A 372 1 O ILE A 370 N PHE A 296 SHEET 5 AA1 7 GLN A 404 THR A 409 1 O GLN A 404 N MET A 369 SHEET 6 AA1 7 THR A 260 CYS A 263 1 N ILE A 262 O GLY A 407 SHEET 7 AA1 7 VAL A 438 ALA A 440 1 O ALA A 440 N CYS A 263 SHEET 1 AA2 6 GLN A 457 LYS A 462 0 SHEET 2 AA2 6 LYS A 737 THR A 742 1 O LEU A 740 N ARG A 461 SHEET 3 AA2 6 LEU A 711 TYR A 715 1 N LEU A 714 O PHE A 739 SHEET 4 AA2 6 THR A 630 PHE A 633 1 N PHE A 633 O ILE A 713 SHEET 5 AA2 6 ILE A 693 ALA A 696 1 O LEU A 694 N LEU A 632 SHEET 6 AA2 6 PRO A 658 LEU A 661 1 N GLY A 659 O ILE A 695 SHEET 1 AA3 3 LEU A 816 TYR A 819 0 SHEET 2 AA3 3 LYS A 807 CYS A 810 -1 N LEU A 808 O CYS A 818 SHEET 3 AA3 3 PHE A 892 VAL A 894 -1 O VAL A 893 N LEU A 809 SHEET 1 AA4 2 VAL A 825 ILE A 826 0 SHEET 2 AA4 2 HIS A 830 TYR A 831 -1 O HIS A 830 N ILE A 826 SHEET 1 AA5 4 PHE A 842 PRO A 846 0 SHEET 2 AA5 4 GLU A 857 CYS A 864 -1 O LYS A 861 N ARG A 845 SHEET 3 AA5 4 ASP A 872 TYR A 879 -1 O HIS A 876 N ALA A 860 SHEET 4 AA5 4 PHE A 882 ILE A 887 -1 O ILE A 884 N VAL A 877 LINK SG CYS A 810 ZN ZN A1001 1555 1555 2.43 LINK SG CYS A 813 ZN ZN A1001 1555 1555 2.31 LINK SG CYS A 864 ZN ZN A1001 1555 1555 2.80 LINK SG CYS A 869 ZN ZN A1001 1555 1555 2.44 SITE 1 AC1 5 CYS A 810 CYS A 813 CYS A 864 CYS A 869 SITE 2 AC1 5 TRP A 873 SITE 1 AC2 1 HIS A 381 CRYST1 175.620 175.620 109.530 90.00 90.00 120.00 P 65 2 2 24 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 0.005694 0.003287 0.000000 0.00000 SCALE2 0.000000 0.006575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009130 0.00000