HEADER DNA 31-AUG-07 2VAH TITLE SOLUTION STRUCTURE OF A B-DNA HAIRPIN AT LOW PRESSURE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*UP*TP COMPND 3 *TP*GP*GP*AP*TP*CP*CP*T)-3'; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: U2 DNA HAIRPIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA, B-DNA HAIRPIN, PRESSURE, NMR EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.P.WILLIAMSON,D.J.WILTON,M.GHOSH,K.V.A.CHARY,K.AKASAKA REVDAT 2 24-FEB-09 2VAH 1 VERSN REVDAT 1 11-SEP-07 2VAH 0 JRNL AUTH M.P.WILLIAMSON,D.J.WILTON,M.GHOSH,K.V.A.CHARY, JRNL AUTH 2 K.AKASAKA JRNL TITL STRUCTURAL CHANGE IN A B-DNA HELIX WITH JRNL TITL 2 HYDROSTATIC PRESSURE JRNL REF NUCLEIC ACIDS RES. V. 36 4032 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18515837 JRNL DOI 10.1093/NAR/GKN350 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE.THIS STRUCTURE IS FOR COMPARISON WITH REMARK 3 THE ACCOMPANYING HIGH PRESSURE STRUCTURE PDB ENTRY 2VAI REMARK 4 REMARK 4 2VAH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-AUG-07. REMARK 100 THE PDBE ID CODE IS EBI-33529. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 MM REMARK 210 PRESSURE : 30.0 BAR REMARK 210 SAMPLE CONTENTS : 90% WATER 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED BY REFINING AN REMARK 210 EXISTING STRUCTURE WITH RESPECT TO LOW PRESSURE PROTON REMARK 210 SHIFT RESTRAINTS 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 H21 DG A 2 - O2 DC A 17 1.57 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 DT A 5 C5 DT A 5 C7 0.052 REMARK 500 DT A 15 C5 DT A 15 C7 0.038 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 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 3 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 4 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DU A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 14 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 14 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 15 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 16 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 17 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DGO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A URACIL CONTAINING REMARK 900 HAIRPIN DNA REMARK 900 RELATED ID: 2VAI RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A B-DNA HAIRPIN AT REMARK 900 HIGH PRESSURE. DBREF 2VAH A 1 18 PDB 2VAH 2VAH 1 18 SEQRES 1 A 18 DA DG DG DA DT DC DC DT DU DT DT DG DG SEQRES 2 A 18 DA DT DC DC DT 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 MASTER 135 0 0 0 0 0 0 6 0 0 0 2 END