HEADER RNA 06-MAR-00 1EJZ TITLE SOLUTION STRUCTURE OF A HNA-RNA HYBRID COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-H(*(6HG)P*(6HC)P*(6HG)P*(6HT)P*(6HA)P*(6HG)P*(6HC) COMPND 7 P*(6HG))-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT D-ARABINO- COMPND 11 HEXITOL SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS HNA-RNA COMPLEX, DOUBLE HELIX, A-TYPE CONFORMATION, RNA EXPDTA SOLUTION NMR AUTHOR E.LESCRNIER,R.ESNOUF,H.A.HEUS,C.W.HILBERS,P.HERDEWIJN REVDAT 4 16-FEB-22 1EJZ 1 REMARK LINK REVDAT 3 24-FEB-09 1EJZ 1 VERSN REVDAT 2 01-APR-03 1EJZ 1 JRNL REVDAT 1 23-OCT-00 1EJZ 0 JRNL AUTH E.LESCRINIER,R.ESNOUF,J.SCHRAML,R.BUSSON,H.HEUS,C.HILBERS, JRNL AUTH 2 P.HERDEWIJN JRNL TITL SOLUTION STRUCTURE OF A HNA-RNA HYBRID. JRNL REF CHEM.BIOL. V. 7 719 2000 JRNL REFN ISSN 1074-5521 JRNL PMID 10980452 JRNL DOI 10.1016/S1074-5521(00)00017-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.DE WINTER,E.LESCRINIER,A.VAN AERSCHOT,P.HERDEWIJN REMARK 1 TITL MINOR GROOVE HYDRATION CONTRIBUTES TO THE RELATIVE STABILITY REMARK 1 TITL 2 OF HNA/RNA HYBRIDS COMPARED TO HNA/DNA COMPLEXES REMARK 1 REF J.AM.CHEM.SOC. V. 120 5381 1998 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA973721F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.3, X-PLOR 3.518 REMARK 3 AUTHORS : VARIAN (VNMR), A.T. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010657. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 20; 5 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.7 MM HNA, 1.7 MM RNA; 1.7 MM REMARK 210 HNA, 1.7 MM RNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; H-P HETCOR; REMARK 210 TOCSY; WATERGATE NOESY; 1D JUMP- REMARK 210 RETURN REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97.0, X-PLOR 3.518 REMARK 210 METHOD USED : TORSION ANGLES DYNAMICS AND REMARK 210 GENTLE MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE CLOSEST TO THE AVERAGE REMARK 210 OF ALL REFINED 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 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 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDI B 17 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EC4 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A HEXITOL NUCLEIC ACID DUPLEX WITH FOUR REMARK 900 CONSECUSTIVE T:T BASE PAIRS DBREF 1EJZ A 1 8 PDB 1EJZ 1EJZ 1 8 DBREF 1EJZ B 9 16 PDB 1EJZ 1EJZ 9 16 SEQRES 1 A 8 C G C U A C G C SEQRES 1 B 8 6HG 6HC 6HG 6HT 6HA 6HG 6HC 6HG MODRES 1EJZ 6HG B 9 DG MODRES 1EJZ 6HC B 10 DC MODRES 1EJZ 6HG B 11 DG MODRES 1EJZ 6HT B 12 DT MODRES 1EJZ 6HA B 13 DA MODRES 1EJZ 6HG B 14 DG MODRES 1EJZ 6HC B 15 DC MODRES 1EJZ 6HG B 16 DG HET 6HG B 9 34 HET 6HC B 10 33 HET 6HG B 11 36 HET 6HT B 12 35 HET 6HA B 13 35 HET 6HG B 14 36 HET 6HC B 15 33 HET 6HG B 16 36 HET PDI B 17 18 HETNAM 6HG 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(GUANIN-9-YL)-6'-O- HETNAM 2 6HG PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HC 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(CYTOSIN-1-YL)-6'-O- HETNAM 2 6HC PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HT 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(THYMIN-1-YL)-6'-O- HETNAM 2 6HT PHOSPHORYL-D-ARABINO-HEXITOL HETNAM 6HA 1',5'-ANHYDRO-2',3'-DIDEOXY-2'-(ADENIN-9-YL)-6'-O- HETNAM 2 6HA PHOSPHORYL-D-ARABINO-HEXITOL HETNAM PDI PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER FORMUL 2 6HG 4(C11 H16 N5 O7 P) FORMUL 2 6HC 2(C10 H16 N3 O7 P) FORMUL 2 6HT C11 H17 N2 O8 P FORMUL 2 6HA C11 H16 N5 O6 P FORMUL 3 PDI C3 H9 O5 P LINK O3' 6HG B 9 P 6HC B 10 1555 1555 1.61 LINK O3' 6HC B 10 P 6HG B 11 1555 1555 1.61 LINK O3' 6HG B 11 P 6HT B 12 1555 1555 1.61 LINK O3' 6HT B 12 P 6HA B 13 1555 1555 1.61 LINK O3' 6HA B 13 P 6HG B 14 1555 1555 1.61 LINK O3' 6HG B 14 P 6HC B 15 1555 1555 1.61 LINK O3' 6HC B 15 P 6HG B 16 1555 1555 1.61 LINK O3' 6HG B 16 P PDI B 17 1555 1555 1.61 SITE 1 AC1 1 6HG B 16 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