Header list of 1s0t.pdb file
Complete list - 2 202 Bytes
HEADER DNA 04-JAN-04 1S0T
TITLE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN ALPHA-ANOMERIC
TITLE 2 ADENOSINE: INSIGHTS INTO SUBSTRATE RECOGNITION BY ENDONUCLEASE IV
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*TP*CP*CP*(A3A)P*CP*GP*AP*CP*G)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*CP*GP*TP*CP*GP*TP*GP*GP*AP*C)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THE CORE OF THE SEQUENCE CORRESPONDS TO THE
SOURCE 4 RECOGNITION SITE OF E. COLI ENDONUCLEASE IV;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES
KEYWDS DNA DOUBLE HELIX WITH ENLARGED MINER GROOVE AND HELICAL KINK, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR J.M.ARAMINI,S.H.CLEAVER,R.T.PON,R.P.CUNNINGHAM,M.W.GERMANN
REVDAT 3 02-MAR-22 1S0T 1 REMARK LINK
REVDAT 2 24-FEB-09 1S0T 1 VERSN
REVDAT 1 20-APR-04 1S0T 0
JRNL AUTH J.M.ARAMINI,S.H.CLEAVER,R.T.PON,R.P.CUNNINGHAM,M.W.GERMANN
JRNL TITL SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN
JRNL TITL 2 ALPHA-ANOMERIC ADENOSINE: INSIGHTS INTO SUBSTRATE
JRNL TITL 3 RECOGNITION BY ENDONUCLEASE IV.
JRNL REF J.MOL.BIOL. V. 338 77 2004
JRNL REFN ISSN 0022-2836
JRNL PMID 15050824
JRNL DOI 10.1016/J.JMB.2004.02.035
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 1.5, AMBER 6.0
REMARK 3 AUTHORS : GUNTERT ET AL (DYANA), CASE ET AL. (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 502 RESTRAINTS: 284 DISTANCE
REMARK 3 RESTRAINTS, 80 ENDOCYCLIC TORSION ANGLE RESTRAINTS, 50 WATSON-
REMARK 3 CRICK DISTANCE AND ANGLE RESTRAINTS,
REMARK 3 AND 88 BACKBONE TORSION ANGLE RESTRAINTS. THE ALPHAA DUPLEX
REMARK 3 STRUCTURE WAS ELUCIDATED BY A COMBINATION OF DYANA AND RMD/REM IN
REMARK 3 AMBER. ALL CALCULATIONS WERE PERFORMED IN VACUO. THE FINAL
REMARK 3 STRUCTURE DEPOSITED HERE WAS OBTAINED BY COORDINATE AVERAGING THE
REMARK 3 FINAL ENSEMBLE OF 10 RMD/REM STRUCTURES FOLLOWED BY RESTRAINED
REMARK 3 ENERGY MINIMIZATION.
REMARK 4
REMARK 4 1S0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-04.
REMARK 100 THE DEPOSITION ID IS D_1000021223.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293; 283
REMARK 210 PH : 6.6; 6.6
REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.0 MM ALPHAA DUPLEX, 10 MM
REMARK 210 PHOSPHATE BUFFER, 50 MM NACL,
REMARK 210 0.1 MM EDTA, PH 6.6; 1.0 MM
REMARK 210 ALPHAA DUPLEX, 10 MM PHOSPHATE
REMARK 210 BUFFER, 50 MM NACL, 0.1 MM EDTA,
REMARK 210 PH 6.6
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY; 2D
REMARK 210 31P,1H CORRELATION; HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : AMX; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS 3.2, CORMA 5.2, CURVES
REMARK 210 5.1, MOLMOL 2.0
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 10
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:
REMARK 210 FOR NON-EXCHANGEABLE PROTONS, NOESY EXPERIMENTS IN D2O WERE
REMARK 210 PERFORMED WITH 10S RELAXATION DELAYS AND MIXING TIMES OF 75MS,
REMARK 210 150MS AND 250 MS.
REMARK 210 FOR EXCHANGEABLE PROTONS, A WATERGATE NOESY WAS PERFORMED WITH A
REMARK 210 RELAXATION DELAY OF 4S AND 150MS MIXING TIME.
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 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 A3A A 5 O3' - P - O5' ANGL. DEV. = -20.4 DEGREES
REMARK 500 DA A 8 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES
REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES
REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG B 18 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES
REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.2 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 DG A 7 0.08 SIDE CHAIN
REMARK 500 DA A 8 0.08 SIDE CHAIN
REMARK 500 DT B 13 0.10 SIDE CHAIN
REMARK 500 DA B 19 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1S74 RELATED DB: PDB
REMARK 900 RELATED ID: 1S75 RELATED DB: PDB
DBREF 1S0T A 1 10 PDB 1S0T 1S0T 1 10
DBREF 1S0T B 11 20 PDB 1S0T 1S0T 11 20
SEQRES 1 A 10 DG DT DC DC A3A DC DG DA DC DG
SEQRES 1 B 10 DC DG DT DC DG DT DG DG DA DC
MODRES 1S0T A3A A 5 DA
HET A3A A 5 32
HETNAM A3A 2'DEOXY-ALPHA-ANOMERIC-ADENOSINE-5'-PHOSPHATE
FORMUL 1 A3A C10 H14 N5 O6 P
LINK O3' DC A 4 P A3A A 5 1555 1555 1.62
LINK O3' A3A A 5 P DC A 6 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
Complete list - 2 202 Bytes