Header list of 1be5.pdb file
Complete list - 16 202 Bytes
HEADER DNA 19-MAY-98 1BE5
TITLE STRUCTURAL STUDIES OF A STABLE PARALLEL-STRANDED DNA DUPLEX
TITLE 2 INCORPORATING ISOGUANINE:CYTOSINE AND ISOCYTOSINE:GUANINE BASE PAIRS
TITLE 3 BY NMR, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA DUPLEX (TGCACGGACT);
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA DUPLEX (TGCACGGACT);
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DNA STRUCTURE, NOVEL DNA BASES, ANTISENSE OLIGONUCLEOTIDES,
KEYWDS 2 INTERCALATOR BINDING, REVERSE WATSON-CRICK BASE PAIRS,
KEYWDS 3 DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
AUTHOR X.-L.YANG,H.SUGIYAMA,S.IKEDA,I.SAITO,A.H.-J.WANG
REVDAT 4 16-FEB-22 1BE5 1 REMARK LINK
REVDAT 3 24-FEB-09 1BE5 1 VERSN
REVDAT 2 01-APR-03 1BE5 1 JRNL
REVDAT 1 12-AUG-98 1BE5 0
JRNL AUTH X.L.YANG,H.SUGIYAMA,S.IKEDA,I.SAITO,A.H.WANG
JRNL TITL STRUCTURAL STUDIES OF A STABLE PARALLEL-STRANDED DNA DUPLEX
JRNL TITL 2 INCORPORATING ISOGUANINE:CYTOSINE AND ISOCYTOSINE:GUANINE
JRNL TITL 3 BASEPAIRS BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY.
JRNL REF BIOPHYS.J. V. 75 1163 1998
JRNL REFN ISSN 0006-3495
JRNL PMID 9726918
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 1BE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000171647.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 275
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 20MM PHOSPHATE BUFFER
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : WATER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY 750; VXR 500
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR, SPEDREF
REMARK 210 METHOD USED : NOE-RMD
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 1H 2D NMR SPECTROSCOPY
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 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 1 C5' DT A 1 C4' 0.069
REMARK 500 DT A 1 C5 DT A 1 C7 0.042
REMARK 500 DT A 10 C5 DT A 10 C7 0.042
REMARK 500 DG B 13 C3' DG B 13 C2' -0.048
REMARK 500 DT B 14 C5' DT B 14 C4' 0.067
REMARK 500 DT B 14 C5 DT B 14 C7 0.039
REMARK 500 DC B 16 C5' DC B 16 C4' 0.055
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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DA A 4 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES
REMARK 500 DG B 15 O4' - C4' - C3' ANGL. DEV. = 5.3 DEGREES
REMARK 500 DG B 15 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES
REMARK 500 DG B 19 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES
REMARK 500 DA B 20 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
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 DT A 10 0.10 SIDE CHAIN
REMARK 500 DG B 15 0.10 SIDE CHAIN
REMARK 500 DA B 20 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1BE5 A 1 10 PDB 1BE5 1BE5 1 10
DBREF 1BE5 B 11 20 PDB 1BE5 1BE5 11 20
SEQRES 1 A 10 DT IGU IMC DA IMC IGU IGU DA IMC DT
SEQRES 1 B 10 DA DC DG DT DG DC DC DT DG DA
MODRES 1BE5 IGU A 2 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
MODRES 1BE5 IMC A 3 DC
MODRES 1BE5 IMC A 5 DC
MODRES 1BE5 IGU A 6 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
MODRES 1BE5 IGU A 7 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
MODRES 1BE5 IMC A 9 DC
HET IGU A 2 33
HET IMC A 3 33
HET IMC A 5 33
HET IGU A 6 33
HET IGU A 7 33
HET IMC A 9 33
HETNAM IGU 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
HETNAM IMC N1-[2-DEOXY-RIBOFURANOSYL]-[2-AMINO-5-METHYL-4-OXO-4H-
HETNAM 2 IMC PYRIMIDINE]-5'-MONOPHOSPHATE
FORMUL 1 IGU 3(C10 H14 N5 O7 P)
FORMUL 1 IMC 3(C10 H16 N3 O7 P)
LINK O3' DT A 1 P IGU A 2 1555 1555 1.61
LINK O3' IGU A 2 P IMC A 3 1555 1555 1.63
LINK O3' IMC A 3 P DA A 4 1555 1555 1.61
LINK O3' DA A 4 P IMC A 5 1555 1555 1.63
LINK O3' IMC A 5 P IGU A 6 1555 1555 1.62
LINK O3' IGU A 6 P IGU A 7 1555 1555 1.62
LINK O3' IGU A 7 P DA A 8 1555 1555 1.62
LINK O3' DA A 8 P IMC A 9 1555 1555 1.63
LINK O3' IMC A 9 P DT A 10 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
Complete list - 16 202 Bytes