HEADER RNA 06-MAR-21 7LYF TITLE DENGUE VIRUS RNA PROMOTER STEM-LOOP A FUSED WITH TRNA-SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PROMOTER STEM-LOOP A FUSED WITH TRNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-32 AND 81-139 FORM THE TRNA SCAFFOLD, WHEREAS COMPND 5 RESIDUES 33-80 MATCH TO RESIDUES 69-116 OF THE DENGUE VIRUS 2 COMPND 6 COMPLETE GENOME GB:KP188569.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11060; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA EXPDTA X-RAY DIFFRACTION AUTHOR E.H.LEE,K.H.CHOI REVDAT 3 18-OCT-23 7LYF 1 REMARK REVDAT 2 19-MAY-21 7LYF 1 JRNL REVDAT 1 12-MAY-21 7LYF 0 JRNL AUTH E.LEE,P.J.BUJALOWSKI,T.TERAMOTO,K.GOTTIPATI,S.D.SCOTT, JRNL AUTH 2 R.PADMANABHAN,K.H.CHOI JRNL TITL STRUCTURES OF FLAVIVIRUS RNA PROMOTERS SUGGEST TWO BINDING JRNL TITL 2 MODES WITH NS5 POLYMERASE. JRNL REF NAT COMMUN V. 12 2530 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33953197 JRNL DOI 10.1038/S41467-021-22846-1 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 10308 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1029 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 33.6880 - 6.4258 0.99 1501 166 0.1860 0.2216 REMARK 3 2 6.4258 - 5.1061 1.00 1409 157 0.2352 0.2904 REMARK 3 3 5.1061 - 4.4623 1.00 1396 154 0.2356 0.2921 REMARK 3 4 4.4623 - 4.0551 1.00 1395 156 0.2594 0.3103 REMARK 3 5 4.0551 - 3.7648 1.00 1353 150 0.2823 0.3184 REMARK 3 6 3.7648 - 3.5431 0.98 1342 150 0.3223 0.3718 REMARK 3 7 3.5431 - 3.4000 0.65 883 96 0.3825 0.4350 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.590 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 155.1 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 : 0.007 3323 REMARK 3 ANGLE : 1.281 5181 REMARK 3 CHIRALITY : 0.057 695 REMARK 3 PLANARITY : 0.007 139 REMARK 3 DIHEDRAL : 18.901 1665 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7LYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255199. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10308 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.366 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.46 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1TN1,5EW4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE PH 6.9, 9% REMARK 280 (W/V) POLYETHYLENE GLYCOL 8000, 200 MM KCL, AND 100 MM MAGNESIUM REMARK 280 ACETATE, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 15.46200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.77900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 168.43850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 15.46200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.77900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 168.43850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 15.46200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.77900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 168.43850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 15.46200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.77900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 168.43850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O2' C A 106 O3' A A 139 8595 2.08 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 G A 1 P G A 1 OP3 -0.121 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 C A 17 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 C A 17 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 C A 17 C2 - N1 - C1' ANGL. DEV. = 8.3 DEGREES REMARK 500 G A 19 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 19 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 G A 19 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 G A 22 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 C A 51 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C A 51 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 57 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 59 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 A A 61 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 A A 61 C8 - N9 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 C A 101 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 C A 101 C2 - N1 - C1' ANGL. DEV. = 7.7 DEGREES REMARK 500 G A 107 C8 - N9 - C4 ANGL. DEV. = 2.7 DEGREES REMARK 500 G A 108 C2 - N3 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 G A 108 N3 - C4 - C5 ANGL. DEV. = 4.8 DEGREES REMARK 500 G A 108 C8 - N9 - C4 ANGL. DEV. = 2.6 DEGREES REMARK 500 G A 108 N3 - C4 - N9 ANGL. DEV. = -4.1 DEGREES REMARK 500 G A 108 C4 - N9 - C1' ANGL. DEV. = -8.4 DEGREES REMARK 500 G A 128 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES REMARK 500 G A 128 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 O6 REMARK 620 2 U A 130 O4 106.7 REMARK 620 N 1 DBREF 7LYF A 1 32 PDB 7LYF 7LYF 1 32 DBREF1 7LYF A 33 80 GB KP188569.1 DBREF2 7LYF A KP188569.1 69 116 DBREF 7LYF A 81 139 PDB 7LYF 7LYF 81 139 SEQRES 1 A 139 G C C C G G A U A G C U C SEQRES 2 A 139 A G U C G G U A G A G C A SEQRES 3 A 139 G C G G A G C U G U U A G SEQRES 4 A 139 U C U A C G U G G A C C G SEQRES 5 A 139 A C A A A G A C A G A U U SEQRES 6 A 139 C U U U G A G G G A G C U SEQRES 7 A 139 A A G C U C A A C G U A G SEQRES 8 A 139 U U C U A A C A G C U C C SEQRES 9 A 139 G C G G G U C C A G G G U SEQRES 10 A 139 U C A A G U C C C U G U U SEQRES 11 A 139 C G G G C G C C A HET MG A 201 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *7(H2 O) LINK O6 G A 5 MG MG A 201 1555 1555 2.01 LINK O4 U A 130 MG MG A 201 1555 1555 2.97 CRYST1 30.924 137.558 336.877 90.00 90.00 90.00 I 2 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 0.032337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002968 0.00000