Header list of 1ho6.pdb file
Complete list - 23 20 Bytes
HEADER DNA, RNA 08-DEC-00 1HO6 TITLE CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*G)-(P*(GAO)P*(UAR) COMPND 3 P*(CAR)P*(CAR)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY KEYWDS ARABINONUCLEIC ACID, RNA, HAIRPIN, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.Y.DENISOV,K.GEHRING REVDAT 4 23-FEB-22 1HO6 1 REMARK LINK REVDAT 3 24-FEB-09 1HO6 1 VERSN REVDAT 2 01-APR-03 1HO6 1 JRNL REVDAT 1 07-NOV-01 1HO6 0 JRNL AUTH A.Y.DENISOV,A.M.NORONHA,C.J.WILDS,J.F.TREMPE,R.T.PON, JRNL AUTH 2 K.GEHRING,M.J.DAMHA JRNL TITL SOLUTION STRUCTURE OF AN ARABINONUCLEIC ACID (ANA)/RNA JRNL TITL 2 DUPLEX IN A CHIMERIC HAIRPIN: COMPARISON WITH JRNL TITL 3 2'-FLUORO-ANA/RNA AND DNA/RNA HYBRIDS. JRNL REF NUCLEIC ACIDS RES. V. 29 4284 2001 JRNL REFN ISSN 0305-1048 JRNL PMID 11691916 JRNL DOI 10.1093/NAR/29.21.4284 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.DAMHA,A.M.NORONHA,C.J.WILDS,J.F.TREMPE,A.Y.DENISOV, REMARK 1 AUTH 2 R.T.PON,K.GEHRING REMARK 1 TITL PROPERTIES OF ARABINONUCLEIC ACIDS (ANA & 2'F-ANA): REMARK 1 TITL 2 IMPLICATIONS FOR THE DESIGN OF ANTISENSE THERAPEUTICS THAT REMARK 1 TITL 3 INVOKE RNASE H CLEAVAGE OF RNA REMARK 1 REF NUCLEOSIDES AND NUCLEOTIDES V. 20 429 2001 REMARK 1 REFN ISSN 0732-8311 REMARK 1 DOI 10.1081/NCN-100002317 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STARTING A- AND B-TYPE STEM HAIRPIN REMARK 3 STRUCTURES WITH RANDOMLY ORGANIZED LOOPS WERE REFINED BY 14 PS REMARK 3 RESTRAINED MOLECULAR DYNAMICS (300-1000 K) WITH FINAL ENEGRY REMARK 3 MINIMIZATION REMARK 4 REMARK 4 1HO6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1000012479. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM HAIRPIN; 1 MM HAIRPIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND REMARK 210 HETERONUCLEAR TECHNIQUES: NOESY, DQF-COSY, TOCSY, H,C-HMQC AND H, REMARK 210 P-HETCOSY 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: CLOSE CONTACTS 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 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 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 DT A 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 5 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 5 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 5 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 104 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FC8 RELATED DB: PDB REMARK 900 1FC8 CONTAINS THE SAME HAIRPIN BUT WITH 2'F-ANA INSTEAD OF ANA REMARK 900 RELATED ID: 1HOQ RELATED DB: PDB REMARK 900 1HOQ CONTAINS THE SAME HAIRPIN BUT WITH RNA/DNA STEM DBREF 1HO6 A 1 12 PDB 1HO6 1HO6 1 12 SEQRES 1 A 12 G G A C DT DT DC DG GAO UAR CAR CAR MODRES 1HO6 GAO A 9 G GUANINE ARABINOSE-5'-PHOSPHATE MODRES 1HO6 UAR A 10 U URACIL ARABINOSE-5'-PHOSPHATE MODRES 1HO6 CAR A 11 DC CYTOSINE ARABINOSE-5'-PHOSPHATE MODRES 1HO6 CAR A 12 DC CYTOSINE ARABINOSE-5'-PHOSPHATE HET GAO A 9 34 HET UAR A 10 30 HET CAR A 11 31 HET CAR A 12 32 HETNAM GAO GUANINE ARABINOSE-5'-PHOSPHATE HETNAM UAR URACIL ARABINOSE-5'-PHOSPHATE HETNAM CAR CYTOSINE ARABINOSE-5'-PHOSPHATE FORMUL 1 GAO C10 H14 N5 O8 P FORMUL 1 UAR C9 H13 N2 O9 P FORMUL 1 CAR 2(C9 H14 N3 O8 P) LINK O3' DG A 8 P GAO A 9 1555 1555 1.61 LINK O3' GAO A 9 P UAR A 10 1555 1555 1.61 LINK O3' UAR A 10 P CAR A 11 1555 1555 1.61 LINK O3' CAR A 11 P CAR A 12 1555 1555 1.61 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 MODEL 1
Complete list - 23 20 Bytes