HEADER RNA 15-APR-19 6OL3 TITLE CRYSTAL STRUCTURE OF AN ADENOVIRUS VIRUS-ASSOCIATED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOVIRUS VIRUS-ASSOCIATED (VA) RNA I APICAL AND CENTRAL COMPND 3 DOMAINS; COMPND 4 CHAIN: C; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN ADENOVIRUS 2; SOURCE 4 ORGANISM_TAXID: 10515 KEYWDS NONCODING RNA, VIRAL RNA, RNA EXPDTA X-RAY DIFFRACTION AUTHOR I.V.HOOD,J.M.GORDON,C.BOU-NADER,F.V.HENDERSON,S.BAHMANJAH,J.ZHANG REVDAT 4 13-MAR-24 6OL3 1 REMARK REVDAT 3 25-DEC-19 6OL3 1 REMARK REVDAT 2 10-JUL-19 6OL3 1 JRNL REVDAT 1 03-JUL-19 6OL3 0 JRNL AUTH I.V.HOOD,J.M.GORDON,C.BOU-NADER,F.E.HENDERSON,S.BAHMANJAH, JRNL AUTH 2 J.ZHANG JRNL TITL CRYSTAL STRUCTURE OF AN ADENOVIRUS VIRUS-ASSOCIATED RNA. JRNL REF NAT COMMUN V. 10 2871 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31253805 JRNL DOI 10.1038/S41467-019-10752-6 REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 18173 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.890 REMARK 3 FREE R VALUE TEST SET COUNT : 2635 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 39.8282 - 7.2972 0.99 1626 143 0.1876 0.1805 REMARK 3 2 7.2972 - 5.7978 1.00 1625 141 0.1937 0.2460 REMARK 3 3 5.7978 - 5.0665 1.00 1626 137 0.1856 0.2078 REMARK 3 4 5.0665 - 4.6040 1.00 1631 132 0.1855 0.2051 REMARK 3 5 4.6040 - 4.2745 1.00 1641 144 0.2089 0.1932 REMARK 3 6 4.2745 - 4.0227 1.00 1601 141 0.1964 0.2284 REMARK 3 7 4.0227 - 3.8214 1.00 1639 141 0.1790 0.2017 REMARK 3 8 3.8214 - 3.6552 1.00 1620 134 0.1796 0.2408 REMARK 3 9 3.6552 - 3.5146 1.00 1629 145 0.2305 0.2377 REMARK 3 10 3.5146 - 3.3933 1.00 1626 140 0.2357 0.2281 REMARK 3 11 3.3933 - 3.2873 1.00 1616 138 0.2055 0.2594 REMARK 3 12 3.2873 - 3.1934 1.00 1642 136 0.2153 0.2696 REMARK 3 13 3.1934 - 3.1093 1.00 1621 136 0.2303 0.2461 REMARK 3 14 3.1093 - 3.0335 1.00 1617 141 0.2542 0.2631 REMARK 3 15 3.0335 - 2.9646 1.00 1623 139 0.3091 0.3392 REMARK 3 16 2.9646 - 2.9015 1.00 1639 144 0.3609 0.3365 REMARK 3 17 2.9015 - 2.8435 1.00 1598 140 0.4028 0.4463 REMARK 3 18 2.8435 - 2.7898 0.97 1563 132 0.4300 0.4127 REMARK 3 19 2.7898 - 2.7400 0.94 1564 131 0.4382 0.4428 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.180 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 : 0.002 2625 REMARK 3 ANGLE : 0.410 4089 REMARK 3 CHIRALITY : 0.022 553 REMARK 3 PLANARITY : 0.002 109 REMARK 3 DIHEDRAL : 11.886 1324 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 26 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.9035 17.2138 -14.9106 REMARK 3 T TENSOR REMARK 3 T11: 1.5072 T22: 0.8142 REMARK 3 T33: 0.6520 T12: -0.0486 REMARK 3 T13: 0.0281 T23: -0.1821 REMARK 3 L TENSOR REMARK 3 L11: -0.0683 L22: 0.1350 REMARK 3 L33: 0.0494 L12: 0.3123 REMARK 3 L13: 0.1929 L23: 0.0536 REMARK 3 S TENSOR REMARK 3 S11: -0.1365 S12: 0.1780 S13: -0.3197 REMARK 3 S21: -0.4025 S22: 0.3085 S23: -0.4350 REMARK 3 S31: 0.5425 S32: 0.0688 S33: -0.1749 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 88 THROUGH 137 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.3387 51.5364 0.9700 REMARK 3 T TENSOR REMARK 3 T11: 0.5901 T22: 0.6438 REMARK 3 T33: 0.2473 T12: 0.0016 REMARK 3 T13: 0.0449 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.9691 L22: 0.6416 REMARK 3 L33: 4.2358 L12: 0.1703 REMARK 3 L13: -0.0417 L23: 0.0613 REMARK 3 S TENSOR REMARK 3 S11: 0.1649 S12: 0.1190 S13: 0.0336 REMARK 3 S21: -0.2103 S22: 0.0222 S23: -0.1130 REMARK 3 S31: 0.1085 S32: 0.5585 S33: -0.1604 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 6OL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : MD2 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 3.64200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: OBELISK CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM CACODYLATE (PH 6.5) 28 REMARK 280 -30% 2-METHYL-2,4-PENTANEDIOL (MPD), PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.35100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.67550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 98.02650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.35100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.02650 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.67550 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 G C 60 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 U C 102 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U C 102 C6 REMARK 470 U C 115 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U C 115 C6 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 K C 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 100 O6 REMARK 620 2 U C 101 O4 73.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K C 201 DBREF 6OL3 C 26 137 PDB 6OL3 6OL3 26 137 SEQRES 1 C 112 G G A C C U C G C A A G G SEQRES 2 C 112 G U A U C A U G G C G G A SEQRES 3 C 112 C G A C C G G G G U U C G SEQRES 4 C 112 A A C C C C G G A U C C G SEQRES 5 C 112 G C C G U C C G C C G U G SEQRES 6 C 112 A U C C A U G C G G U U A SEQRES 7 C 112 C C G C C C G C G U G U C SEQRES 8 C 112 G A A C C C A G G U G U G SEQRES 9 C 112 C G A G G U C C HET K C 201 1 HETNAM K POTASSIUM ION FORMUL 2 K K 1+ FORMUL 3 HOH *9(H2 O) LINK O6 G C 100 K K C 201 1555 1555 3.26 LINK O4 U C 101 K K C 201 1555 1555 3.11 SITE 1 AC1 2 G C 100 U C 101 CRYST1 100.455 100.455 130.702 90.00 90.00 90.00 P 41 2 2 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 0.009955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007651 0.00000