PDB Short entry for 1Z2J HEADER RNA 08-MAR-05 1Z2J TITLE SOLUTION STRUCTURE OF THE HIV-1 FRAMESHIFT INDUCING ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 FRAMESHIFT SITE RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PRODUCED FROM IN VITRO TRANSCRIPTON WITH T7 SOURCE 4 RNA PLOYMERASE FROM DNA TEMPLATES. KEYWDS STEM-LOOP, PURINE BULGE, TETRALOOP, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.W.STAPLE,S.E.BUTCHER REVDAT 3 02-MAR-22 1Z2J 1 REMARK REVDAT 2 24-FEB-09 1Z2J 1 VERSN REVDAT 1 14-JUN-05 1Z2J 0 JRNL AUTH D.W.STAPLE,S.E.BUTCHER JRNL TITL SOLUTION STRUCTURE AND THERMODYNAMIC INVESTIGATION OF THE JRNL TITL 2 HIV-1 FRAMESHIFT INDUCING ELEMENT. JRNL REF J.MOL.BIOL. V. 349 1011 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15927637 JRNL DOI 10.1016/J.JMB.2005.03.038 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z2J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032216. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 283 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : ALL NMR SAMPLES WERE 1 MM RNA, REMARK 210 AND APPROXIMATELY 50 MM NACL, REMARK 210 100% D2O; ALL NMR SAMPLES WERE 1 REMARK 210 MM RNA, AND APPROXIMATELY 50 MM REMARK 210 NACL, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNN-COSY; HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE, SPARKY, CNS REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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' A A 22 O4' A A 23 1.39 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 10 A A 33 C4' A A 33 C3' -0.064 REMARK 500 11 A A 33 C4' A A 33 C3' -0.062 REMARK 500 20 A A 33 C4' A A 33 C3' -0.071 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 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 2 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 3 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 3 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 4 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 5 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 5 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 5 C A 31 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 6 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 7 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 7 C A 31 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 8 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 8 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 9 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 9 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 9 C A 31 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 10 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 11 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 12 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 12 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 13 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 14 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 15 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 16 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 17 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 17 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 18 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 18 A A 28 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 19 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 20 G A 11 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 20 A A 22 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PJY RELATED DB: PDB REMARK 900 HIV-1 FRAMESHIFT SITE STEM-LOOP DBREF 1Z2J A 1 45 PDB 1Z2J 1Z2J 1 45 SEQRES 1 A 45 G G G A A G A U C U G G C SEQRES 2 A 45 C U U C C C A C A A G G G SEQRES 3 A 45 A A G G C C A G G G A A U SEQRES 4 A 45 C U U C C C 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