Header list of 1d0t.pdb file
Complete list - 16 20 Bytes
HEADER RNA 14-SEP-99 1D0T
TITLE SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SITE FOR
TITLE 2 PHAGE MS2 COAT PROTEIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 RNA BINDING SITE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: MS2 REPLICASE OPERATOR HAIRPIN. RP PHOSPHORYL (NON-
COMPND 6 BRIDGING) SULFUR 5' TO EACH ADENINE NUCLEOTIDE.
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: TRANSCRIPTION BY T7 RNA PLOYMERASE USING 5'-A-THIO-
SOURCE 4 ATP
KEYWDS RNA HAIRPIN, PHOSPHOROTHIOATE, THIOPHOSPHATE, BULGED BASE, STEM-LOOP,
KEYWDS 2 RNA
EXPDTA SOLUTION NMR
NUMMDL 10
MDLTYP MINIMIZED AVERAGE
AUTHOR J.S.SMITH,E.P.NIKONOWICZ
REVDAT 3 16-FEB-22 1D0T 1 REMARK LINK
REVDAT 2 24-FEB-09 1D0T 1 VERSN
REVDAT 1 24-MAY-00 1D0T 0
JRNL AUTH J.S.SMITH,E.P.NIKONOWICZ
JRNL TITL PHOSPHOROTHIOATE SUBSTITUTION CAN SUBSTANTIALLY ALTER RNA
JRNL TITL 2 CONFORMATION.
JRNL REF BIOCHEMISTRY V. 39 5642 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 10801314
JRNL DOI 10.1021/BI992712B
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : UXNMR 1994, X-PLOR 3.851
REMARK 3 AUTHORS : SPECTRASPIN (UXNMR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED USING 313
REMARK 3 CONFORMATIONALLY RESTRICTIVE NOE DISTANCE CONSTRAINTS (I.E.,
REMARK 3 INTRA-RESIDUE SUGAR-SUGAR NOES ARE NOT INCLUDED), 20 H-BOND BASE
REMARK 3 PAIR CONSTRAINTS, 30 BACKBONE DIHEDRAL RESTRAINTS, AND DIHEDRAL
REMARK 3 RESTRAINTS TO RESTRICT SUGAR PUCKER CONFORMATION. PARAMETER FILE
REMARK 3 WAS MODIFIED TO INCORPORATE BOND-LENGTH, BOND-ANGLE, CHARGE, VAN
REMARK 3 DER WAAL'S RADIUS FOR THE RP PHOSPHORYL SULFUR ATOMS LOCATED 5'
REMARK 3 TO EACH ADENINE IN THE SEQUENCE. [JAROSZEWSKI, JW., ET AL., ANTI-
REMARK 3 CANCER DRUG DESIGN ( 1992) 7, 253; FLORIAN, J. ET AL., J. AM.
REMARK 3 CHEM. SOC. (1998) 120, 7959].
REMARK 4
REMARK 4 1D0T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-99.
REMARK 100 THE DEPOSITION ID IS D_1000009692.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : ~50MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2.0 MM REPLICASE OPERATOR RNA U
REMARK 210 -15N,13C AT U, C, AND G,
REMARK 210 UNLABELED A; PHOSPHOROTHIOATE 5'
REMARK 210 TO EACH ADENINE;; 10 MM KPI
REMARK 210 BUFFER; 10 MM NACL; 0.2 MM EDTA;
REMARK 210 2.0 MM REPLICASE OPERATOR RNA U-
REMARK 210 15N,13C AT U, C, AND G,
REMARK 210 UNLABELED A; PHOSPHOROTHIOATE 5'
REMARK 210 TO EACH ADENINE;; 10 MM KPI
REMARK 210 BUFFER; 10 MM NACL; 0.2 MM EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; DQF-COSY; 31P-
REMARK 210 1H HETCOR; 2D 13C-FILTERED NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 1998, X-PLOR 3.851
REMARK 210 METHOD USED : SIMULATED ANNEALING AND
REMARK 210 MOLECULAR DYNAMICS REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 30
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM,
REMARK 210 STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH THE LEAST RESTRAINT
REMARK 210 VIOLATIONS, STRUCTURES WITH THE
REMARK 210 LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR
REMARK 210 AND 2D/3D HETERONUCLEAR TECHNIQUES. FILTERED EXPERIMENTS USED TO
REMARK 210 IDENTIFY INTER-RESIDUE NOES INVOLVING UNLABELED A RESIDUES
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: 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. = 4.6 DEGREES
REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 3 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 3 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 3 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 3 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 4 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 4 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 4 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 4 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 4 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 4 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 5 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 5 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 120 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1D0U RELATED DB: PDB
REMARK 900 PHAGE MS2 REPLICASE OPERATOR RNA HAIRPIN
DBREF 1D0T A 1 21 PDB 1D0T 1D0T 1 21
SEQRES 1 A 21 G G G SRA U C SRA C C SRA U U SRA
SEQRES 2 A 21 G G G SRA U C U C
MODRES 1D0T SRA A 4 A ADENOSINE -5'-THIO-MONOPHOSPHATE
MODRES 1D0T SRA A 7 A ADENOSINE -5'-THIO-MONOPHOSPHATE
MODRES 1D0T SRA A 10 A ADENOSINE -5'-THIO-MONOPHOSPHATE
MODRES 1D0T SRA A 13 A ADENOSINE -5'-THIO-MONOPHOSPHATE
MODRES 1D0T SRA A 17 A ADENOSINE -5'-THIO-MONOPHOSPHATE
HET SRA A 4 33
HET SRA A 7 33
HET SRA A 10 33
HET SRA A 13 33
HET SRA A 17 33
HETNAM SRA ADENOSINE -5'-THIO-MONOPHOSPHATE
FORMUL 1 SRA 5(C10 H14 N5 O6 P S)
LINK O3' G A 3 P SRA A 4 1555 1555 1.61
LINK O3' SRA A 4 P U A 5 1555 1555 1.61
LINK O3' C A 6 P SRA A 7 1555 1555 1.61
LINK O3' SRA A 7 P C A 8 1555 1555 1.61
LINK O3' C A 9 P SRA A 10 1555 1555 1.61
LINK O3' SRA A 10 P U A 11 1555 1555 1.61
LINK O3' U A 12 P SRA A 13 1555 1555 1.61
LINK O3' SRA A 13 P G A 14 1555 1555 1.61
LINK O3' G A 16 P SRA A 17 1555 1555 1.61
LINK O3' SRA A 17 P U A 18 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 - 16 20 Bytes