HEADER PEPTIDE NUCLEIC ACID 15-MAR-10 2KVJ TITLE NMR AND MD SOLUTION STRUCTURE OF A GAMMA-METHYLATED PNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-MODIFIED PEPTIDE NUCLEIC ACID; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS PNA, GAMMA-METHYLATED PNA, METHYL MODIFIED PNA, PEPTIDE NUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR W.HE,M.J.CRAWFORD,S.RAPIREDDY,M.MADRID,R.R.GIL,D.H.LY,C.ACHIM REVDAT 3 22-SEP-10 2KVJ 1 JRNL REVDAT 2 19-MAY-10 2KVJ 1 JRNL REMARK REVDAT 1 12-MAY-10 2KVJ 0 JRNL AUTH W.HE,M.J.CRAWFORD,S.RAPIREDDY,M.MADRID,R.R.GIL,D.H.LY, JRNL AUTH 2 C.ACHIM JRNL TITL THE STRUCTURE OF A GAMMA-MODIFIED PEPTIDE NUCLEIC ACID JRNL TITL 2 DUPLEX. JRNL REF MOL BIOSYST V. 6 1619 2010 JRNL REFN ISSN 1742-206X JRNL PMID 20386807 JRNL DOI 10.1039/C002254C REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 2 NS RESTRAINED MD REMARK 4 REMARK 4 2KVJ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB101625. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 17.6 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : [DSPNA]=0.4 MM PEPTIDE NUCLEIC REMARK 210 ACID-1, 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 10 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : MODEL 1 IS THE AVERAGE OF 10 NMR REMARK 210 -DETERMINED STRUCTURES 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K4G RELATED DB: PDB REMARK 900 GAMMA-METHYLATED PNA DUPLEX DBREF 2KVJ A 1 10 PDB 2KVJ 2KVJ 1 10 DBREF 2KVJ B 11 20 PDB 2KVJ 2KVJ 11 20 SEQRES 1 A 10 ACE 40G 40G 40C 40A 40T 40G 40C 40C NME SEQRES 1 B 10 ACE 40G 40G 40C 40A 40T 40G 40C 40C NME HET ACE A 1 6 HET 40G A 2 37 HET 40G A 3 37 HET 40C A 4 34 HET 40A A 5 36 HET 40T A 6 36 HET 40G A 7 37 HET 40C A 8 34 HET 40C A 9 34 HET NME A 10 6 HET ACE B 11 6 HET 40G B 12 37 HET 40G B 13 37 HET 40C B 14 34 HET 40A B 15 36 HET 40T B 16 36 HET 40G B 17 37 HET 40C B 18 34 HET 40C B 19 34 HET NME B 20 6 HETNAM ACE ACETYL GROUP HETNAM 40G N-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)ACETYL]-N- HETNAM 2 40G [(2S)-2-AMINOPROPYL]GLYCINE HETNAM 40C N-[(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)ACETYL]-N-[(2S)-2- HETNAM 2 40C AMINOPROPYL]GLYCINE HETNAM 40A N-[(2S)-2-AMINOPROPYL]-N-[(6-AMINO-9H-PURIN-9-YL) HETNAM 2 40A ACETYL]GLYCINE HETNAM 40T N-[(2S)-2-AMINOPROPYL]-N-[(5-METHYL-2,4-DIOXO-3,4- HETNAM 2 40T DIHYDROPYRIMIDIN-1(2H)-YL)ACETYL]GLYCINE HETNAM NME METHYLAMINE FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 40G 6(C12 H17 N7 O4) FORMUL 1 40C 6(C11 H17 N5 O4) FORMUL 1 40A 2(C12 H17 N7 O3) FORMUL 1 40T 2(C12 H18 N4 O5) FORMUL 1 NME 2(C H5 N) LINK C' 40C B 19 N NME B 20 1555 1555 1.21 LINK C' 40G A 2 N1' 40G A 3 1555 1555 1.31 LINK C' 40G A 3 N1' 40C A 4 1555 1555 1.26 LINK C' 40C A 4 N1' 40A A 5 1555 1555 1.32 LINK C' 40A A 5 N1' 40T A 6 1555 1555 1.32 LINK C' 40T A 6 N1' 40G A 7 1555 1555 1.32 LINK C' 40G A 7 N1' 40C A 8 1555 1555 1.32 LINK C' 40C A 8 N1' 40C A 9 1555 1555 1.31 LINK C' 40G B 12 N1' 40G B 13 1555 1555 1.31 LINK C' 40G B 13 N1' 40C B 14 1555 1555 1.32 LINK C' 40C B 14 N1' 40A B 15 1555 1555 1.27 LINK C' 40A B 15 N1' 40T B 16 1555 1555 1.32 LINK C' 40T B 16 N1' 40G B 17 1555 1555 1.32 LINK C' 40G B 17 N1' 40C B 18 1555 1555 1.32 LINK C' 40C B 18 N1' 40C B 19 1555 1555 1.31 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 72 0 20 0 0 0 0 6 0 0 0 2 END