Header list of 1okf.pdb file
Complete list - 25 20 Bytes
HEADER DNA-RNA HYBRID 23-JUL-03 1OKF
TITLE NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*ATLP*GP*AP*ATLP*AP*ATLP*GP*CP)-3';
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ALPHA-L-LNA;
COMPND 5 OTHER_DETAILS: ALPHA-L-LNA THYMINE MODIFICATIONS AT
COMPND 6 POSITIONS 2,5 AND 7;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: 5'-R(*GP*CP*AP*UP*AP*UP*CP*AP*GP)-3';
COMPND 9 CHAIN: B
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DNA-RNA HYBRID, DNA/RNA HYBRID, ALPHA-L-LNA, LNA, RNA, NMR,
KEYWDS 2 RNASE H, LOCKED NUCLEIC ACID
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.T.NIELSEN,P.C.STEIN,M.PETERSEN
REVDAT 2 24-FEB-09 1OKF 1 VERSN
REVDAT 1 09-OCT-03 1OKF 0
JRNL AUTH J.T.NIELSEN,P.C.STEIN,M.PETERSEN
JRNL TITL NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID:
JRNL TITL 2 STRUCTURAL IMPLICATIONS FOR RNASE H RECOGNITION
JRNL REF NUCLEIC ACIDS RES. V. 31 5858 2003
JRNL REFN ISSN 0305-1048
JRNL PMID 14530434
JRNL DOI 10.1093/NAR/GKG800
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,
REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN
REMARK 3 THE JRNL CITATION ABOVE
REMARK 4
REMARK 4 1OKF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUL-03.
REMARK 100 THE PDBE ID CODE IS EBI-13158.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 100 MM NACL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 3 MM NUCLEIC ACID, 100 MM NACL,
REMARK 210 10 MM PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX, AMBER
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 16
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 1H,1H-NOES FROM
REMARK 210 NOESY AND WATERGATE NOESY EXPERIMENTS
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: 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 1 DA A 4 C5' DA A 4 C4' 0.062
REMARK 500 2 DA A 4 C5' DA A 4 C4' 0.062
REMARK 500 3 DA A 4 C5' DA A 4 C4' 0.063
REMARK 500 4 DA A 4 C5' DA A 4 C4' 0.060
REMARK 500 5 DA A 4 C5' DA A 4 C4' 0.062
REMARK 500 6 DA A 4 C5' DA A 4 C4' 0.061
REMARK 500 7 DA A 4 C5' DA A 4 C4' 0.060
REMARK 500 8 DA A 4 C5' DA A 4 C4' 0.063
REMARK 500 9 DA A 4 C5' DA A 4 C4' 0.061
REMARK 500 10 DA A 4 C5' DA A 4 C4' 0.061
REMARK 500 11 DA A 4 C5' DA A 4 C4' 0.063
REMARK 500 12 DA A 4 C5' DA A 4 C4' 0.061
REMARK 500 13 DA A 4 C5' DA A 4 C4' 0.063
REMARK 500 14 DA A 4 C5' DA A 4 C4' 0.058
REMARK 500 15 DA A 4 C5' DA A 4 C4' 0.061
REMARK 500 16 DA A 4 C5' DA A 4 C4' 0.063
REMARK 500 17 DA A 4 C5' DA A 4 C4' 0.061
REMARK 500 18 DA A 4 C5' DA A 4 C4' 0.062
REMARK 500 19 DA A 4 C5' DA A 4 C4' 0.062
REMARK 500 20 DA A 4 C5' DA A 4 C4' 0.061
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = -2.4 DEGREES
REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DG A 3 O3' - P - OP1 ANGL. DEV. = -16.9 DEGREES
REMARK 500 1 DG A 3 O3' - P - OP2 ANGL. DEV. = -16.9 DEGREES
REMARK 500 1 DG A 3 C3' - O3' - P ANGL. DEV. = -9.8 DEGREES
REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DA A 6 O4' - C1' - C2' ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DA A 6 O3' - P - OP1 ANGL. DEV. = -26.1 DEGREES
REMARK 500 1 DA A 6 O3' - P - OP2 ANGL. DEV. = -26.1 DEGREES
REMARK 500 1 DA A 6 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DG A 8 C3' - C2' - C1' ANGL. DEV. = 8.2 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DG A 8 O3' - P - O5' ANGL. DEV. = 14.1 DEGREES
REMARK 500 1 DG A 8 O3' - P - OP1 ANGL. DEV. = -24.5 DEGREES
REMARK 500 1 DG A 8 O3' - P - OP2 ANGL. DEV. = -24.5 DEGREES
REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 U B 15 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 A B 17 C3' - C2' - C1' ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 A B 17 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 G B 18 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = -2.1 DEGREES
REMARK 500 2 DG A 3 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DG A 3 O3' - P - OP1 ANGL. DEV. = -15.6 DEGREES
REMARK 500 2 DG A 3 O3' - P - OP2 ANGL. DEV. = -15.6 DEGREES
REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = -10.6 DEGREES
REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DA A 6 O4' - C1' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DA A 6 O3' - P - OP1 ANGL. DEV. = -25.9 DEGREES
REMARK 500 2 DA A 6 O3' - P - OP2 ANGL. DEV. = -25.9 DEGREES
REMARK 500 2 DA A 6 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES
REMARK 500 2 DG A 8 C3' - C2' - C1' ANGL. DEV. = 8.4 DEGREES
REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 DG A 8 O3' - P - O5' ANGL. DEV. = 14.7 DEGREES
REMARK 500 2 DG A 8 O3' - P - OP1 ANGL. DEV. = -24.4 DEGREES
REMARK 500 2 DG A 8 O3' - P - OP2 ANGL. DEV. = -24.4 DEGREES
REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 U B 15 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES
REMARK 500 2 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 A B 17 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES
REMARK 500 2 G B 18 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = -3.0 DEGREES
REMARK 500 3 DG A 3 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES
REMARK 500 3 DG A 3 O3' - P - OP1 ANGL. DEV. = -23.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 465 ANGLE DEVIATIONS
REMARK 500
REMARK 500 REMARK: NULL
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 1 DC A 1 0.08 SIDE CHAIN
REMARK 500 1 A B 17 0.11 SIDE CHAIN
REMARK 500 2 DC A 1 0.08 SIDE CHAIN
REMARK 500 2 A B 17 0.12 SIDE CHAIN
REMARK 500 3 DC A 1 0.07 SIDE CHAIN
REMARK 500 3 DC A 9 0.07 SIDE CHAIN
REMARK 500 3 A B 17 0.10 SIDE CHAIN
REMARK 500 4 DC A 1 0.07 SIDE CHAIN
REMARK 500 4 A B 17 0.10 SIDE CHAIN
REMARK 500 5 DC A 1 0.09 SIDE CHAIN
REMARK 500 5 A B 17 0.12 SIDE CHAIN
REMARK 500 6 DC A 1 0.07 SIDE CHAIN
REMARK 500 6 A B 17 0.10 SIDE CHAIN
REMARK 500 7 DC A 1 0.07 SIDE CHAIN
REMARK 500 7 A B 17 0.10 SIDE CHAIN
REMARK 500 8 DC A 1 0.08 SIDE CHAIN
REMARK 500 8 A B 17 0.10 SIDE CHAIN
REMARK 500 9 DC A 1 0.07 SIDE CHAIN
REMARK 500 9 A B 17 0.11 SIDE CHAIN
REMARK 500 10 DC A 1 0.07 SIDE CHAIN
REMARK 500 10 A B 17 0.10 SIDE CHAIN
REMARK 500 11 DC A 1 0.09 SIDE CHAIN
REMARK 500 11 A B 17 0.11 SIDE CHAIN
REMARK 500 11 G B 18 0.05 SIDE CHAIN
REMARK 500 12 DC A 1 0.06 SIDE CHAIN
REMARK 500 12 A B 17 0.11 SIDE CHAIN
REMARK 500 13 DC A 1 0.08 SIDE CHAIN
REMARK 500 13 A B 17 0.11 SIDE CHAIN
REMARK 500 14 DC A 1 0.08 SIDE CHAIN
REMARK 500 14 DG A 3 0.07 SIDE CHAIN
REMARK 500 14 A B 17 0.12 SIDE CHAIN
REMARK 500 15 DC A 1 0.07 SIDE CHAIN
REMARK 500 15 A B 17 0.11 SIDE CHAIN
REMARK 500 16 DC A 1 0.08 SIDE CHAIN
REMARK 500 16 A B 17 0.11 SIDE CHAIN
REMARK 500 17 DC A 1 0.08 SIDE CHAIN
REMARK 500 17 A B 17 0.09 SIDE CHAIN
REMARK 500 17 G B 18 0.06 SIDE CHAIN
REMARK 500 18 DC A 1 0.09 SIDE CHAIN
REMARK 500 18 A B 17 0.10 SIDE CHAIN
REMARK 500 19 DC A 1 0.06 SIDE CHAIN
REMARK 500 19 A B 17 0.11 SIDE CHAIN
REMARK 500 20 DC A 1 0.08 SIDE CHAIN
REMARK 500 20 DC A 9 0.06 SIDE CHAIN
REMARK 500 20 A B 17 0.12 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1OKF A 1 9 PDB 1OKF 1OKF 1 9
DBREF 1OKF B 10 18 PDB 1OKF 1OKF 10 18
SEQRES 1 A 9 DC ATL DG DA ATL DA ATL DG DC
SEQRES 1 B 9 G C A U A U C A G
MODRES 1OKF ATL A 2 T MODIFIED THYMINE
MODRES 1OKF ATL A 5 T MODIFIED THYMINE
MODRES 1OKF ATL A 7 T MODIFIED THYMINE
HET ATL A 2 34
HET ATL A 5 34
HET ATL A 7 34
HETNAM ATL [(1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-
HETNAM 2 ATL DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL
HETNAM 3 ATL DIHYDROGEN PHOSPHATE
FORMUL 1 ATL 3(C11 H15 N2 O9 P)
LINK O3' DC A 1 P ATL A 2 1555 1555 1.62
LINK O3' ATL A 2 P DG A 3 1555 1555 1.60
LINK O3' DA A 4 P ATL A 5 1555 1555 1.63
LINK O3' ATL A 5 P DA A 6 1555 1555 1.62
LINK O3' DA A 6 P ATL A 7 1555 1555 1.62
LINK O3' ATL A 7 P DG A 8 1555 1555 1.63
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 - 25 20 Bytes