HEADER DNA/PEPTIDE NUCLEIC ACID 24-JAN-03 1NR8 TITLE THE CRYSTAL STRUCTURE OF A D-LYSINE-BASED CHIRAL PNA-DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(P*AP*GP*TP*GP*AP*TP*CP*TP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: H-((GPN)*(TPN)*(APN)*(GPN)*(A66)*(T66)*(C66)*(APN)*(CPN) COMPND 8 *(TPN))-NH2; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PEPTIDE NUCLEIC ACID SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS CHIRAL PEPTIDE NUCLEIC ACID, DOUBLE STRANDED HELIX, P-FORM, DNA- KEYWDS 2 PEPTIDE NUCLEIC ACID COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.MENCHISE,G.DE SIMONE,T.TEDESCHI,R.CORRADINI,S.SFORZA,R.MARCHELLI, AUTHOR 2 D.CAPASSO,M.SAVIANO,C.PEDONE REVDAT 4 15-NOV-23 1NR8 1 REMARK LINK ATOM REVDAT 3 13-JUL-11 1NR8 1 VERSN REVDAT 2 24-FEB-09 1NR8 1 VERSN REVDAT 1 28-OCT-03 1NR8 0 JRNL AUTH V.MENCHISE,G.DE SIMONE,T.TEDESCHI,R.CORRADINI,S.SFORZA, JRNL AUTH 2 R.MARCHELLI,D.CAPASSO,M.SAVIANO,C.PEDONE JRNL TITL INSIGHTS INTO PEPTIDE NUCLEIC ACID (PNA) STRUCTURAL JRNL TITL 2 FEATURES: THE CRYSTAL STRUCTURE OF A D-LYSINE-BASED CHIRAL JRNL TITL 3 PNA-DNA DUPLEX JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 12021 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 14512516 JRNL DOI 10.1073/PNAS.2034746100 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.MENCHISE,G.DE SIMONE,R.CORRADINI,S.SFORZA,S.SORRENTINO, REMARK 1 AUTH 2 A.ROMANELLI,M.SAVIANO,C.PEDONE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF REMARK 1 TITL 2 A D-LYSINE-BASED CHIRAL PNA-DNA DUPLEX REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 553 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444902001427 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 5429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 579 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 413 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.110 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NR8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-02; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.3; 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ELETTRA REMARK 200 BEAMLINE : ID14-1; 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.200; 0.918 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18500 REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K. ISOPROPANOL, MAGNESIUM CHLORIDE, MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.93333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.86667 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 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 NH2 B 11 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA A 9 0.07 SIDE CHAIN 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 B9001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GPN B 4 N3 REMARK 620 2 A66 B 5 N1' 120.1 REMARK 620 3 HOH B9017 O 90.8 117.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 9001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PDT RELATED DB: PDB REMARK 900 AN ACHIRAL PNA-DNA NMR STRUCTURE REMARK 900 RELATED ID: 1PUP RELATED DB: PDB REMARK 900 AN ACHIRAL PNA-PNA CRYSTAL STRUCTURE DBREF 1NR8 A 1 10 PDB 1NR8 1NR8 1 10 DBREF 1NR8 B 1 11 PDB 1NR8 1NR8 1 11 SEQRES 1 A 10 DA DG DT DG DA DT DC DT DA DC SEQRES 1 B 11 GPN TPN APN GPN A66 T66 C66 APN CPN TPN NH2 MODRES 1NR8 GPN B 1 DG MODRES 1NR8 TPN B 2 DT MODRES 1NR8 APN B 3 DA MODRES 1NR8 GPN B 4 DG MODRES 1NR8 APN B 8 DA MODRES 1NR8 CPN B 9 DC MODRES 1NR8 TPN B 10 DT HET GPN B 1 21 HET TPN B 2 19 HET APN B 3 20 HET GPN B 4 21 HET A66 B 5 25 HET T66 B 6 24 HET C66 B 7 23 HET APN B 8 20 HET CPN B 9 18 HET TPN B 10 19 HET NH2 B 11 1 HET MG B9001 1 HETNAM GPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE HETNAM TPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE HETNAM APN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE HETNAM A66 2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-ADENINE HETNAM T66 2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-THYMINE HETNAM C66 2-AMINOETHYLLYSINE-CARBONYLMETHYLENE-CYTOSINE HETNAM CPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE HETNAM NH2 AMINO GROUP HETNAM MG MAGNESIUM ION FORMUL 2 GPN 2(C11 H16 N7 O4 1+) FORMUL 2 TPN 2(C11 H17 N4 O5 1+) FORMUL 2 APN 2(C11 H16 N7 O3 1+) FORMUL 2 A66 C15 H24 N8 O3 FORMUL 2 T66 C15 H25 N5 O5 FORMUL 2 C66 C14 H24 N6 O4 FORMUL 2 CPN C10 H16 N5 O4 1+ FORMUL 2 NH2 H2 N FORMUL 3 MG MG 2+ FORMUL 4 HOH *80(H2 O) LINK C GPN B 1 N TPN B 2 1555 1555 1.33 LINK C TPN B 2 N APN B 3 1555 1555 1.33 LINK C APN B 3 N GPN B 4 1555 1555 1.34 LINK C GPN B 4 N1' A66 B 5 1555 1555 1.33 LINK C' A66 B 5 N1' T66 B 6 1555 1555 1.34 LINK C' T66 B 6 N1' C66 B 7 1555 1555 1.32 LINK C' C66 B 7 N APN B 8 1555 1555 1.34 LINK C APN B 8 N CPN B 9 1555 1555 1.33 LINK C CPN B 9 N TPN B 10 1555 1555 1.33 LINK C TPN B 10 N NH2 B 11 1555 1555 1.32 LINK N3 GPN B 4 MG MG B9001 1555 1555 2.85 LINK N1' A66 B 5 MG MG B9001 1555 1555 3.10 LINK MG MG B9001 O HOH B9017 1555 1555 2.81 SITE 1 AC1 3 GPN B 4 A66 B 5 HOH B9017 CRYST1 34.940 34.940 35.800 90.00 90.00 120.00 P 31 3 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 0.028622 0.016525 0.000000 0.00000 SCALE2 0.000000 0.033050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027935 0.00000