Header list of 1ntq.pdb file
Complete list - 23 202 Bytes
HEADER DNA/RNA 30-JAN-03 1NTQ
TITLE 5'(DCCUCCUU)3':3'(RAGGAGGAAA)5'
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*CP*CP*UP*CP*CP*UP*U)-3';
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, RNA, HYBRID, PROPYNYL, DNA-RNA COMPLEX
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR B.M.ZNOSKO,T.W.BARNES III,T.R.KRUGH,D.H.TURNER
REVDAT 3 23-FEB-22 1NTQ 1 REMARK
REVDAT 2 24-FEB-09 1NTQ 1 VERSN
REVDAT 1 10-JUN-03 1NTQ 0
JRNL AUTH B.M.ZNOSKO,T.W.BARNES III,T.R.KRUGH,D.H.TURNER
JRNL TITL NMR STUDIES OF DNA SINGLE STRANDS AND DNA:RNA HYBRIDS WITH
JRNL TITL 2 AND WITHOUT 1-PROPYNYLATION AT C5 OF OLIGOPYRIMIDINES
JRNL REF J.AM.CHEM.SOC. V. 125 6090 2003
JRNL REFN ISSN 0002-7863
JRNL PMID 12785839
JRNL DOI 10.1021/JA021285D
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH T.W.BARNES III,D.H.TURNER
REMARK 1 TITL LONG-RANGE COOPERATIVITY IN MOLECULAR RECOGNITION OF RNA BY
REMARK 1 TITL 2 OLIGODEOXYNUCLEOTIDES WITH MULTIPLE C5-(1-PROPYNYL)
REMARK 1 TITL 3 PYRIMIDINES
REMARK 1 REF J.AM.CHEM.SOC. V. 123 4107 2001
REMARK 1 REFN ISSN 0002-7863
REMARK 1 DOI 10.1021/JA003208T
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 5.2, DISCOVER 95.0
REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF
REMARK 3 140 INTERPROTON DISTANCE RESTRAINTS, 18 HYDROGEN BOND RESTRAINTS,
REMARK 3 AND 104 DIHEDRAL ANGLE RESTRAINTS.
REMARK 4
REMARK 4 1NTQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-03.
REMARK 100 THE DEPOSITION ID IS D_1000018194.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 273; 303
REMARK 210 PH : 7.0; 7.0
REMARK 210 IONIC STRENGTH : 80 MM NACL; 80 MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : ~1MM HYBRID, 80 MM NACL, 10 MM
REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA,
REMARK 210 90% H2O, 10% D2O; ~2.5 MM HYBRID,
REMARK 210 80 MM NACL, 10 MM PHOSPHATE,
REMARK 210 0.5 MM EDTA, 99.996% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 2000, DISCOVER 95.0
REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY
REMARK 210 MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
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 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 A A 2 N3 A A 2 C4 0.122
REMARK 500 A A 2 C4 A A 2 C5 0.078
REMARK 500 A A 2 N7 A A 2 C8 0.067
REMARK 500 A A 3 N3 A A 3 C4 0.120
REMARK 500 A A 3 C4 A A 3 C5 0.077
REMARK 500 A A 3 N7 A A 3 C8 0.068
REMARK 500 A A 4 N3 A A 4 C4 0.122
REMARK 500 A A 4 C4 A A 4 C5 0.077
REMARK 500 A A 4 N7 A A 4 C8 0.069
REMARK 500 G A 5 N1 G A 5 C2 0.094
REMARK 500 G A 5 N3 G A 5 C4 0.098
REMARK 500 G A 5 C4 G A 5 C5 0.058
REMARK 500 G A 5 C5 G A 5 C6 0.130
REMARK 500 G A 5 N7 G A 5 C8 0.070
REMARK 500 G A 6 N1 G A 6 C2 0.092
REMARK 500 G A 6 N3 G A 6 C4 0.095
REMARK 500 G A 6 C4 G A 6 C5 0.058
REMARK 500 G A 6 C5 G A 6 C6 0.132
REMARK 500 G A 6 N7 G A 6 C8 0.072
REMARK 500 A A 7 N3 A A 7 C4 0.122
REMARK 500 A A 7 C4 A A 7 C5 0.075
REMARK 500 A A 7 N7 A A 7 C8 0.066
REMARK 500 G A 8 N1 G A 8 C2 0.093
REMARK 500 G A 8 N3 G A 8 C4 0.096
REMARK 500 G A 8 C4 G A 8 C5 0.058
REMARK 500 G A 8 C5 G A 8 C6 0.132
REMARK 500 G A 8 N7 G A 8 C8 0.072
REMARK 500 G A 9 N1 G A 9 C2 0.093
REMARK 500 G A 9 N3 G A 9 C4 0.096
REMARK 500 G A 9 C4 G A 9 C5 0.057
REMARK 500 G A 9 C5 G A 9 C6 0.130
REMARK 500 G A 9 N7 G A 9 C8 0.071
REMARK 500 A A 10 N3 A A 10 C4 0.121
REMARK 500 A A 10 C4 A A 10 C5 0.075
REMARK 500 A A 10 N7 A A 10 C8 0.068
REMARK 500 DC B 1 C4 DC B 1 N4 0.072
REMARK 500 DC B 1 N1 DC B 1 C6 0.131
REMARK 500 DC B 1 C2 DC B 1 N3 0.117
REMARK 500 DC B 1 C4 DC B 1 C5 -0.056
REMARK 500 DC B 2 C4 DC B 2 N4 0.072
REMARK 500 DC B 2 N1 DC B 2 C6 0.130
REMARK 500 DC B 2 C2 DC B 2 N3 0.116
REMARK 500 DC B 2 C4 DC B 2 C5 -0.056
REMARK 500 DU B 3 N1 DU B 3 C6 0.118
REMARK 500 DU B 3 C4 DU B 3 C5 0.115
REMARK 500 DC B 4 C4 DC B 4 N4 0.071
REMARK 500 DC B 4 N1 DC B 4 C6 0.129
REMARK 500 DC B 4 C2 DC B 4 N3 0.117
REMARK 500 DC B 4 C4 DC B 4 C5 -0.056
REMARK 500 DC B 5 C4 DC B 5 N4 0.071
REMARK 500
REMARK 500 THIS ENTRY HAS 57 BOND DEVIATIONS.
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 A A 2 C2 - N3 - C4 ANGL. DEV. = 5.2 DEGREES
REMARK 500 A A 2 N3 - C4 - C5 ANGL. DEV. = -9.4 DEGREES
REMARK 500 A A 2 C5 - N7 - C8 ANGL. DEV. = -6.4 DEGREES
REMARK 500 A A 2 N7 - C8 - N9 ANGL. DEV. = 8.6 DEGREES
REMARK 500 A A 2 C8 - N9 - C4 ANGL. DEV. = -6.5 DEGREES
REMARK 500 A A 2 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES
REMARK 500 A A 2 N3 - C4 - N9 ANGL. DEV. = 7.0 DEGREES
REMARK 500 A A 3 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES
REMARK 500 A A 3 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES
REMARK 500 A A 3 N3 - C4 - C5 ANGL. DEV. = -9.2 DEGREES
REMARK 500 A A 3 C5 - N7 - C8 ANGL. DEV. = -6.6 DEGREES
REMARK 500 A A 3 N7 - C8 - N9 ANGL. DEV. = 8.4 DEGREES
REMARK 500 A A 3 C8 - N9 - C4 ANGL. DEV. = -6.0 DEGREES
REMARK 500 A A 3 N3 - C4 - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 A A 4 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES
REMARK 500 A A 4 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES
REMARK 500 A A 4 N3 - C4 - C5 ANGL. DEV. = -9.3 DEGREES
REMARK 500 A A 4 C5 - N7 - C8 ANGL. DEV. = -6.4 DEGREES
REMARK 500 A A 4 N7 - C8 - N9 ANGL. DEV. = 8.3 DEGREES
REMARK 500 A A 4 C8 - N9 - C4 ANGL. DEV. = -6.1 DEGREES
REMARK 500 A A 4 N3 - C4 - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 G A 5 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES
REMARK 500 G A 5 C2 - N3 - C4 ANGL. DEV. = 11.2 DEGREES
REMARK 500 G A 5 N3 - C4 - C5 ANGL. DEV. = -10.9 DEGREES
REMARK 500 G A 5 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G A 5 C4 - C5 - N7 ANGL. DEV. = 2.7 DEGREES
REMARK 500 G A 5 C5 - N7 - C8 ANGL. DEV. = -7.2 DEGREES
REMARK 500 G A 5 N7 - C8 - N9 ANGL. DEV. = 8.8 DEGREES
REMARK 500 G A 5 C8 - N9 - C4 ANGL. DEV. = -6.9 DEGREES
REMARK 500 G A 5 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES
REMARK 500 G A 5 N3 - C4 - N9 ANGL. DEV. = 8.3 DEGREES
REMARK 500 G A 5 C6 - C5 - N7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 G A 5 C5 - C6 - O6 ANGL. DEV. = -5.0 DEGREES
REMARK 500 G A 6 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES
REMARK 500 G A 6 C2 - N3 - C4 ANGL. DEV. = 11.2 DEGREES
REMARK 500 G A 6 N3 - C4 - C5 ANGL. DEV. = -10.8 DEGREES
REMARK 500 G A 6 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 G A 6 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES
REMARK 500 G A 6 C5 - N7 - C8 ANGL. DEV. = -7.1 DEGREES
REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 8.7 DEGREES
REMARK 500 G A 6 C8 - N9 - C4 ANGL. DEV. = -6.9 DEGREES
REMARK 500 G A 6 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES
REMARK 500 G A 6 N3 - C4 - N9 ANGL. DEV. = 8.0 DEGREES
REMARK 500 G A 6 C5 - C6 - O6 ANGL. DEV. = -4.8 DEGREES
REMARK 500 A A 7 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES
REMARK 500 A A 7 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES
REMARK 500 A A 7 N3 - C4 - C5 ANGL. DEV. = -9.3 DEGREES
REMARK 500 A A 7 C5 - N7 - C8 ANGL. DEV. = -6.5 DEGREES
REMARK 500 A A 7 N7 - C8 - N9 ANGL. DEV. = 8.5 DEGREES
REMARK 500 A A 7 C8 - N9 - C4 ANGL. DEV. = -6.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 107 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 A A 2 0.08 SIDE CHAIN
REMARK 500 G A 9 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1NTS RELATED DB: PDB
REMARK 900 DNA:RNA HYBRID WITH PROPYNYLATED BASES 1-7 IN DNA STRAND
REMARK 900 RELATED ID: 1NTT RELATED DB: PDB
REMARK 900 DNA:RNA HYBRID WITH PROPYNYLATED BASES 2-7 IN DNA STRAND
DBREF 1NTQ A 2 10 PDB 1NTQ 1NTQ 2 10
DBREF 1NTQ B 1 7 PDB 1NTQ 1NTQ 1 7
SEQRES 1 A 9 A A A G G A G G A
SEQRES 1 B 7 DC DC DU DC DC DU DU
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 - 23 202 Bytes