Header list of 2dd3.pdb file
Complete list - 9 20 Bytes
HEADER RNA 19-JAN-06 2DD3
TITLE AN ALTERNATING SHEARED AA PAIR IN 5'GGUGAAGGCU/3'PCCGAAGCCG: II. THE
TITLE 2 MINOR CONFORMATION WITH A6/A5/A16 STACK
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(P5P))-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 RAPID CONFORMATION EXCHANGE, ALTERNATING SHEARED AA PAIR, SEQUENCE
KEYWDS 2 SPECIFIC A-MINOR MOTIF, KINK-TURN MOTIF, THERMODYNAMICS, RNA
KEYWDS 3 SECONDARY STRUCTURE PREDICTION, RNA
EXPDTA SOLUTION NMR
NUMMDL 18
AUTHOR G.CHEN,S.D.KENNEDY,T.R.KRUGH,D.H.TURNER
REVDAT 4 09-MAR-22 2DD3 1 REMARK LINK
REVDAT 3 21-JUL-09 2DD3 1 HET HETATM HETNAM MODRES
REVDAT 3 2 1 FORMUL LINK SEQRES COMPND
REVDAT 2 24-FEB-09 2DD3 1 VERSN
REVDAT 1 13-JUN-06 2DD3 0
JRNL AUTH G.CHEN,S.D.KENNEDY,J.QIAO,T.R.KRUGH,D.H.TURNER
JRNL TITL AN ALTERNATING SHEARED AA PAIR AND ELEMENTS OF STABILITY FOR
JRNL TITL 2 A SINGLE SHEARED PURINE-PURINE PAIR FLANKED BY SHEARED GA
JRNL TITL 3 PAIRS IN RNA
JRNL REF BIOCHEMISTRY V. 45 6889 2006
JRNL REFN ISSN 0006-2960
JRNL PMID 16734425
JRNL DOI 10.1021/BI0524464
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DISCOVER
REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2DD3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JAN-06.
REMARK 100 THE DEPOSITION ID IS D_1000025272.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : 80MM NACL, 10MM SODIUM
REMARK 210 PHOSPHATE, 0.5MM NA2EDTA, 2MM
REMARK 210 TOTAL DUPLEX CONCENTRATIONS, PH
REMARK 210 5.1, PD 7.3
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX, VNMR
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY, STRUCTURES WITH THE
REMARK 210 LEAST RESTRAINT VIOLATIONS
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 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 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 2 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 2 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 3 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 3 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 3 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 4 U A 3 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 4 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 4 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 4 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 5 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 5 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 5 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 5 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 6 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 6 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 6 G A 7 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 6 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 6 U A 10 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 6 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 6 C B 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 6 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 7 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 7 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 7 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 7 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 7 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 8 U A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 8 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 8 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 8 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 9 U A 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 9 U A 10 C5' - C4' - O4' ANGL. DEV. = 6.3 DEGREES
REMARK 500 9 U A 10 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES
REMARK 500 9 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 9 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 10 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 10 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 10 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 10 C B 13 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 10 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 11 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 91 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 A A 5 0.06 SIDE CHAIN
REMARK 500 1 A B 15 0.06 SIDE CHAIN
REMARK 500 2 A A 5 0.07 SIDE CHAIN
REMARK 500 2 G B 11 0.06 SIDE CHAIN
REMARK 500 2 G B 14 0.05 SIDE CHAIN
REMARK 500 2 A B 16 0.07 SIDE CHAIN
REMARK 500 3 A B 15 0.07 SIDE CHAIN
REMARK 500 4 G B 14 0.06 SIDE CHAIN
REMARK 500 4 A B 15 0.06 SIDE CHAIN
REMARK 500 5 A A 5 0.07 SIDE CHAIN
REMARK 500 5 G B 11 0.06 SIDE CHAIN
REMARK 500 5 A B 15 0.07 SIDE CHAIN
REMARK 500 5 A B 16 0.07 SIDE CHAIN
REMARK 500 6 A B 16 0.09 SIDE CHAIN
REMARK 500 7 A A 5 0.08 SIDE CHAIN
REMARK 500 7 G B 11 0.06 SIDE CHAIN
REMARK 500 7 G B 14 0.07 SIDE CHAIN
REMARK 500 8 A A 5 0.05 SIDE CHAIN
REMARK 500 8 A A 6 0.06 SIDE CHAIN
REMARK 500 8 G A 7 0.08 SIDE CHAIN
REMARK 500 8 G A 8 0.07 SIDE CHAIN
REMARK 500 8 A B 15 0.07 SIDE CHAIN
REMARK 500 9 A A 6 0.06 SIDE CHAIN
REMARK 500 9 G A 7 0.07 SIDE CHAIN
REMARK 500 9 G A 8 0.07 SIDE CHAIN
REMARK 500 9 G B 11 0.06 SIDE CHAIN
REMARK 500 9 A B 15 0.08 SIDE CHAIN
REMARK 500 11 A A 5 0.08 SIDE CHAIN
REMARK 500 11 G A 8 0.06 SIDE CHAIN
REMARK 500 11 A B 15 0.06 SIDE CHAIN
REMARK 500 12 A A 5 0.08 SIDE CHAIN
REMARK 500 12 A B 15 0.08 SIDE CHAIN
REMARK 500 13 A B 15 0.07 SIDE CHAIN
REMARK 500 14 G B 14 0.07 SIDE CHAIN
REMARK 500 15 G A 4 0.09 SIDE CHAIN
REMARK 500 15 G B 11 0.06 SIDE CHAIN
REMARK 500 15 G B 14 0.08 SIDE CHAIN
REMARK 500 15 A B 16 0.06 SIDE CHAIN
REMARK 500 16 G B 11 0.06 SIDE CHAIN
REMARK 500 16 A B 16 0.08 SIDE CHAIN
REMARK 500 17 G A 4 0.05 SIDE CHAIN
REMARK 500 17 A A 6 0.06 SIDE CHAIN
REMARK 500 18 G B 14 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2DD1 RELATED DB: PDB
REMARK 900 3 SHEARED GA PAIRS CLOSED BY UA AND CG WC PAIRS, 5'GGUGGAGGCU/3'
REMARK 900 PCCAAAGCCG
REMARK 900 RELATED ID: 2DD2 RELATED DB: PDB
REMARK 900 5'GGUGAAGGCU/3'PCCGAAGCCG
REMARK 900 RELATED ID: 1XV0 RELATED DB: PDB
REMARK 900 3 SHEARED GA PAIRS CLOSED BY UG WOBBLE AND CG WC PAIRS, 5'
REMARK 900 GGUGGAGGCU/3'PCCGAAGCCG
DBREF 2DD3 A 1 10 PDB 2DD3 2DD3 1 10
DBREF 2DD3 B 11 20 PDB 2DD3 2DD3 11 20
SEQRES 1 A 10 G G U G A A G G C U
SEQRES 1 B 10 G C C G A A G C C P5P
MODRES 2DD3 P5P B 20 A PURINE RIBOSIDE-5'-MONOPHOSPHATE
HET P5P B 20 32
HETNAM P5P PURINE RIBOSIDE-5'-MONOPHOSPHATE
FORMUL 2 P5P C10 H13 N4 O7 P
LINK O3' C B 19 P P5P B 20 1555 1555 1.62
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 - 9 20 Bytes