HEADER RNA 05-FEB-04 1S9S TITLE SOLUTION STRUCTURE OF MLV PSI SITE CAVEAT 1S9S CHIRALITY ERRORS IN MODELS 10, 14, 20. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MLV PSI ENCAPSIDATION SITE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STEM LOOP BCD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY IN VITRO SOURCE 4 TRANSCRIPTION USING A LINEARIZED DNA PLASMID AS TEMPLATE AND T7 RNA SOURCE 5 POLYMERASE KEYWDS MLV, A-MINOR K-TURN, STEM LOOP, BULGE, G-U MISMATCH, G-A MISMATCH, U- KEYWDS 2 U MISMATCH, A-C MISMATCH, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.D'SOUZA,A.DEY,D.HABIB,M.F.SUMMERS REVDAT 4 22-MAY-24 1S9S 1 REMARK REVDAT 3 02-MAR-22 1S9S 1 REMARK REVDAT 2 24-FEB-09 1S9S 1 VERSN REVDAT 1 06-APR-04 1S9S 0 JRNL AUTH V.D'SOUZA,A.DEY,D.HABIB,M.F.SUMMERS JRNL TITL NMR STRUCTURE OF THE 101-NUCLEOTIDE CORE ENCAPSIDATION JRNL TITL 2 SIGNAL OF THE MOLONEY MURINE LEUKEMIA VIRUS. JRNL REF J.MOL.BIOL. V. 337 427 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15003457 JRNL DOI 10.1016/J.JMB.2004.01.037 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA REMARK 3 AUTHORS : BRUKER (XWINNMR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S9S COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021545. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 283; 308; 308; 308; 283; REMARK 210 308; 308; 308; 283; 308; 308 REMARK 210 PH : 7.0; 7.0; 7.0; 7.0; 7.0; 7.0; REMARK 210 7.0; 7.0; 7.0; 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 5 MM NACL; 5 MM NACL; 5 MM NACL; REMARK 210 5 MM NACL; 5 MM NACL; 5 MM NACL; REMARK 210 5 MM NACL; 5 MM NACL; 5 MM NACL; REMARK 210 5 MM NACL; 5 MM NACL; 5 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM PSI MONOMERIC RNA GUA REMARK 210 -15N,13C, 10MM TRIS, 100% D2O; REMARK 210 1.2 MM PSI MONOMERIC RNA ADE-15N, REMARK 210 13C, 10MM TRIS, 100% D2O; 1.2 MM REMARK 210 PSI MONOMERIC RNA URA-15N,13C, REMARK 210 10MM TRIS, 100% D2O; 1.2 MM PSI REMARK 210 MONOMERIC RNA CYT-15N,13C, 10MM REMARK 210 TRIS, 100% D2O; 1.2 MM PSI REMARK 210 MONOMERIC RNA GUA-URA-15N, 90% REMARK 210 H2O, 10% D2O; 1.2 MM PSI REMARK 210 MONOMERIC RNA GUA-URA-CYT-2H, REMARK 210 10MM TRIS, 100% D2O; 1.2 MM PSI REMARK 210 MONOMERIC RNA GUA-URA-ADE-2H, REMARK 210 10MM TRIS, 100% D2O; 1.2 MM PSI REMARK 210 MONOMERIC RNA GUA-CYT-ADE-2H, REMARK 210 10MM TRIS, 100% D2O; 1.2 MM PSI REMARK 210 MONOMERIC RNA ADE-URA-CYT-2H, REMARK 210 10MM TRIS, 100% D2O; 0.6 MM SL-B REMARK 210 MONOMERIC RNA 15N,13C, 10MM TRIS, REMARK 210 0.1 MM EDTA, 100% D2O; 0.6 MM REMARK 210 SL-C MONOMERIC RNA 15N,13C, 10MM REMARK 210 TRIS, 0.1 MM EDTA, 100% D2O; 0.6 REMARK 210 MM SL-D MONOMERIC RNA 15N,13C, REMARK 210 10MM TRIS, 0.1 MM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D ROESY; 2D HMQC; REMARK 210 3D_13C-SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY; 2D WATERGATE REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.0.3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 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 ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO2' C A 301 H5' U A 302 1.24 REMARK 500 HO2' A A 341 H5' C A 342 1.31 REMARK 500 HO2' G A 351 H5' C A 352 1.35 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 1 G A 276 O4' G A 276 C4' -0.170 REMARK 500 1 G A 277 O4' G A 277 C4' -0.247 REMARK 500 1 C A 278 O4' C A 278 C4' -0.216 REMARK 500 1 U A 281 O4' U A 281 C4' -0.083 REMARK 500 1 U A 287 O4' U A 287 C4' -0.085 REMARK 500 1 U A 288 O4' U A 288 C4' -0.110 REMARK 500 1 A A 290 O4' A A 290 C4' -0.126 REMARK 500 1 A A 293 O4' A A 293 C4' -0.140 REMARK 500 1 C A 295 O4' C A 295 C4' -0.090 REMARK 500 1 U A 300 O4' U A 300 C4' -0.102 REMARK 500 1 U A 302 O4' U A 302 C4' -0.101 REMARK 500 1 G A 303 O4' G A 303 C4' -0.192 REMARK 500 1 U A 304 O4' U A 304 C4' -0.099 REMARK 500 1 G A 310 O4' G A 310 C4' -0.191 REMARK 500 1 G A 313 O4' G A 313 C4' -0.149 REMARK 500 1 A A 314 O4' A A 314 C4' -0.126 REMARK 500 1 C A 315 O4' C A 315 C4' -0.299 REMARK 500 1 G A 318 O4' G A 318 C4' -0.183 REMARK 500 1 U A 328 O4' U A 328 C4' -0.154 REMARK 500 1 G A 339 O4' G A 339 C4' -0.324 REMARK 500 1 A A 341 O4' A A 341 C4' -0.227 REMARK 500 1 G A 351 O4' G A 351 C4' -0.094 REMARK 500 1 G A 363 O4' G A 363 C4' -0.125 REMARK 500 1 A A 364 O4' A A 364 C4' -0.117 REMARK 500 1 G A 366 O4' G A 366 C4' -0.084 REMARK 500 2 G A 276 O4' G A 276 C4' -0.190 REMARK 500 2 G A 277 O4' G A 277 C4' -0.244 REMARK 500 2 C A 278 O4' C A 278 C4' -0.186 REMARK 500 2 G A 280 O4' G A 280 C4' -0.099 REMARK 500 2 U A 281 O4' U A 281 C4' -0.104 REMARK 500 2 U A 287 O4' U A 287 C4' -0.108 REMARK 500 2 U A 288 O4' U A 288 C4' -0.129 REMARK 500 2 G A 289 O4' G A 289 C4' -0.105 REMARK 500 2 A A 290 O4' A A 290 C4' -0.108 REMARK 500 2 G A 291 O4' G A 291 C4' -0.079 REMARK 500 2 A A 292 O4' A A 292 C4' -0.151 REMARK 500 2 C A 295 O4' C A 295 C4' -0.080 REMARK 500 2 U A 300 O4' U A 300 C4' -0.101 REMARK 500 2 C A 301 O4' C A 301 C4' -0.103 REMARK 500 2 U A 302 O4' U A 302 C4' -0.123 REMARK 500 2 G A 303 O4' G A 303 C4' -0.178 REMARK 500 2 U A 304 O4' U A 304 C4' -0.085 REMARK 500 2 G A 310 O4' G A 310 C4' -0.205 REMARK 500 2 G A 313 O4' G A 313 C4' -0.158 REMARK 500 2 A A 314 O4' A A 314 C4' -0.131 REMARK 500 2 C A 315 O4' C A 315 C4' -0.305 REMARK 500 2 C A 316 O4' C A 316 C4' -0.112 REMARK 500 2 C A 317 O4' C A 317 C4' -0.122 REMARK 500 2 G A 318 O4' G A 318 C4' -0.171 REMARK 500 2 U A 330 O4' U A 330 C4' -0.327 REMARK 500 REMARK 500 THIS ENTRY HAS 618 BOND DEVIATIONS. 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 1 G A 276 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 G A 276 C1' - O4' - C4' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 G A 276 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 276 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 276 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 277 C5' - C4' - O4' ANGL. DEV. = 19.7 DEGREES REMARK 500 1 G A 277 C1' - O4' - C4' ANGL. DEV. = 11.2 DEGREES REMARK 500 1 G A 277 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 277 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 277 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 278 C5' - C4' - O4' ANGL. DEV. = 12.6 DEGREES REMARK 500 1 C A 278 C1' - O4' - C4' ANGL. DEV. = 10.5 DEGREES REMARK 500 1 G A 279 O4' - C4' - C3' ANGL. DEV. = -9.7 DEGREES REMARK 500 1 G A 279 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 G A 279 C6 - N1 - C2 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 G A 279 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 279 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 280 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 G A 280 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 280 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 280 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 280 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 281 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 U A 281 C1' - O4' - C4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 A A 282 O4' - C4' - C3' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 A A 282 C1' - O4' - C4' ANGL. DEV. = 7.7 DEGREES REMARK 500 1 C A 283 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 C A 283 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 U A 284 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 U A 284 C1' - O4' - C4' ANGL. DEV. = 8.2 DEGREES REMARK 500 1 A A 285 O4' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 1 A A 285 C1' - O4' - C4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 G A 286 O4' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 G A 286 C1' - O4' - C4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 G A 286 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 286 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 286 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 287 O4' - C4' - C3' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 U A 287 C1' - O4' - C4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 U A 288 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 U A 288 C1' - O4' - C4' ANGL. DEV. = 8.7 DEGREES REMARK 500 1 G A 289 O4' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 G A 289 C1' - O4' - C4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 G A 289 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 289 N1 - C2 - N3 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 289 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 A A 290 C1' - O4' - C4' ANGL. DEV. = 9.2 DEGREES REMARK 500 1 G A 291 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 291 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 291 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 5910 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1S9S A 276 376 PDB 1S9S 1S9S 276 376 SEQRES 1 A 101 G G C G G U A C U A G U U SEQRES 2 A 101 G A G A A A C U A G C U C SEQRES 3 A 101 U G U A U C U G G C G G A SEQRES 4 A 101 C C C G U G G U G G A A C SEQRES 5 A 101 U G U G A A G U U C G G A SEQRES 6 A 101 A C A C C C G G C C G C A SEQRES 7 A 101 A C C C U G G G A G A G G SEQRES 8 A 101 U C C C A G G G U U CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1