HEADER PEPTIDE NUCLEIC ACID 07-JUN-08 2K4G TITLE SOLUTION STRUCTURE OF A PEPTIDE NUCLEIC ACID DUPLEX, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PNA (N'-(*(GPN)*(GPN)*(CPN)*(APN)*(TPN)*(GPN)*(CPN)*(CPN))- COMPND 3 C'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS PEPTIDE NUCLEIC ACID, PNA, PNA-PNA DUPLEX, LEFT-HANDED DUPLEX, P-FORM EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR W.HE,E.HATCHER,A.BALAEFF,D.BERATAN,R.GIL,M.MADRID,C.ACHIM REVDAT 4 13-JUL-11 2K4G 1 VERSN REVDAT 3 24-FEB-09 2K4G 1 VERSN REVDAT 2 14-OCT-08 2K4G 1 JRNL REVDAT 1 23-SEP-08 2K4G 0 JRNL AUTH W.HE,E.HATCHER,A.BALAEFF,D.N.BERATAN,R.R.GIL,M.MADRID, JRNL AUTH 2 C.ACHIM JRNL TITL SOLUTION STRUCTURE OF A PEPTIDE NUCLEIC ACID DUPLEX FROM NMR JRNL TITL 2 DATA: FEATURES AND LIMITATIONS. JRNL REF J.AM.CHEM.SOC. V. 130 13264 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 18781753 JRNL DOI 10.1021/JA800652H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MODEL 1 IS THE MINIMIZED AVERAGE OF 10 REMARK 3 STRUCTURES (MODELS 2 TO 11). STRUCTURES HAVE NO MISSING ATOMS. REMARK 3 HOWEVER, REMARK 470 AND 610 WERE ADDED AUTOMATICALLY DUE TO PDB REMARK 3 CONVENTIONS. REMARK 4 REMARK 4 2K4G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB100663. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM SS PNA, 10 MM SODIUM REMARK 210 PHOSPHATE 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 9 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS IN EXPLICIT SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-11 REMARK 470 RES CSSEQI ATOMS REMARK 470 CPN A 9 OXT REMARK 470 CPN B 9 OXT REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NME A 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NME B 10 DBREF 2K4G A 2 9 PDB 2K4G 2K4G 2 9 DBREF 2K4G B 2 9 PDB 2K4G 2K4G 2 9 SEQRES 1 A 9 ACE GPN GPN CPN APN TPN GPN CPN CPN SEQRES 1 B 9 ACE GPN GPN CPN APN TPN GPN CPN CPN MODRES 2K4G GPN A 2 DG MODRES 2K4G GPN A 3 DG MODRES 2K4G CPN A 4 DC MODRES 2K4G APN A 5 DA MODRES 2K4G TPN A 6 DT MODRES 2K4G GPN A 7 DG MODRES 2K4G CPN A 8 DC MODRES 2K4G CPN A 9 DC MODRES 2K4G GPN B 2 DG MODRES 2K4G GPN B 3 DG MODRES 2K4G CPN B 4 DC MODRES 2K4G APN B 5 DA MODRES 2K4G TPN B 6 DT MODRES 2K4G GPN B 7 DG MODRES 2K4G CPN B 8 DC MODRES 2K4G CPN B 9 DC HET ACE A 1 6 HET GPN A 2 34 HET GPN A 3 34 HET CPN A 4 31 HET APN A 5 33 HET TPN A 6 33 HET GPN A 7 34 HET CPN A 8 31 HET CPN A 9 31 HET ACE B 1 6 HET GPN B 2 34 HET GPN B 3 34 HET CPN B 4 31 HET APN B 5 33 HET TPN B 6 33 HET GPN B 7 34 HET CPN B 8 31 HET CPN B 9 31 HET NME A 10 6 HET NME B 10 6 HETNAM ACE ACETYL GROUP HETNAM GPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE HETNAM CPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE HETNAM APN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE HETNAM TPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE HETNAM NME METHYLAMINE FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 GPN 6(C11 H16 N7 O4 1+) FORMUL 1 CPN 6(C10 H16 N5 O4 1+) FORMUL 1 APN 2(C11 H16 N7 O3 1+) FORMUL 1 TPN 2(C11 H17 N4 O5 1+) FORMUL 3 NME 2(C H5 N) LINK C ACE A 1 N1' GPN A 2 1555 1555 1.35 LINK C' GPN A 2 N1' GPN A 3 1555 1555 1.35 LINK C' GPN A 3 N1' CPN A 4 1555 1555 1.35 LINK C' CPN A 4 N1' APN A 5 1555 1555 1.35 LINK C' APN A 5 N1' TPN A 6 1555 1555 1.35 LINK C' TPN A 6 N1' GPN A 7 1555 1555 1.35 LINK C' GPN A 7 N1' CPN A 8 1555 1555 1.35 LINK C' CPN A 8 N1' CPN A 9 1555 1555 1.35 LINK C' CPN A 9 N NME A 10 1555 1555 1.34 LINK C ACE B 1 N1' GPN B 2 1555 1555 1.34 LINK C' GPN B 2 N1' GPN B 3 1555 1555 1.35 LINK C' GPN B 3 N1' CPN B 4 1555 1555 1.35 LINK C' CPN B 4 N1' APN B 5 1555 1555 1.35 LINK C' APN B 5 N1' TPN B 6 1555 1555 1.35 LINK C' TPN B 6 N1' GPN B 7 1555 1555 1.35 LINK C' GPN B 7 N1' CPN B 8 1555 1555 1.35 LINK C' CPN B 8 N1' CPN B 9 1555 1555 1.35 LINK C' CPN B 9 N NME B 10 1555 1555 1.34 SITE 1 AC1 1 GPN B 2 SITE 1 AC2 2 CPN A 8 CPN A 9 SITE 1 AC3 2 GPN A 2 CPN B 9 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 90 0 20 0 0 0 3 6 0 0 0 2 END