Header list of 1s75.pdb file
Complete list - 2 202 Bytes
HEADER DNA 28-JAN-04 1S75 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 1S75 1 REMARK LINK REVDAT 2 24-FEB-09 1S75 1 VERSN REVDAT 1 20-APR-04 1S75 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 6.1 REMARK 3 AUTHORS : GUNTERT ET AL (DYANA), CASE ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 502 RESTRAINTS: 284 DISTANCE RESTRAINTS, 80 ENDOCYCLIC TORSION REMARK 3 ANGLE RESTRAINTS, 50 WATSON-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 REMARK 3 IN AMBER. ALL CALCULATIONS WERE PERFORMED IN VACUO. THE FINAL REMARK 3 STRUCTURE DEPOSITED HERE WAS OBTAINED BY COORDINATE AVERAGING REMARK 3 THE FINAL ENSEMBLE OF 10 RMD/REM STRUCTURES FOLLOWED BY REMARK 3 RESTRAINED ENERGY MINIMIZATION. THE IN VACUO STRUCTURE WAS THEN REMARK 3 SOLVATED IN A SOLVENT BOX AND NA+ COUNTERIONS. THE FOLLOWING REMARK 3 SIMULATIONS CONTAINED 25 C-H RESIDUAL DIPOLAR COUPLINGS REMARK 3 RESTRAINTS. THE FINAL SOLVATED STRUCTURE WAS OBTAINED BY REMARK 3 AVERAGING THE LAST 5PS OF A 1 NS RMD RUN FOLLOWED BY REM. REMARK 4 REMARK 4 1S75 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021451. 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; 13C,1H 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, REMARK 210 MOLECULAR DYNAMICS 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: FOR NON-EXCHANGEABLE PROTONS, NOESY EXPERIMENTS IN D2O REMARK 210 WERE PERFORMED WITH 10S RELAXATION DELAYS AND MIXING TIMES OF REMARK 210 75MS, 150MS AND 250 MS. FOR EXCHANGEABLE PROTONS, A WATERGATE REMARK 210 NOESY WAS PERFORMED WITH A RELAXATION DELAY OF 4S AND 150MS REMARK 210 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. = -3.9 DEGREES REMARK 500 A3A A 5 O3' - P - O5' ANGL. DEV. = -23.4 DEGREES REMARK 500 DC A 6 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 8 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC A 9 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 3.1 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. = 2.3 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 1 0.06 SIDE CHAIN REMARK 500 DG A 7 0.09 SIDE CHAIN REMARK 500 DA A 8 0.12 SIDE CHAIN REMARK 500 DT B 13 0.12 SIDE CHAIN REMARK 500 DA B 19 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S0T RELATED DB: PDB REMARK 900 RELATED ID: 1S74 RELATED DB: PDB DBREF 1S75 A 1 10 PDB 1S75 1S75 1 10 DBREF 1S75 B 11 20 PDB 1S75 1S75 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 1S75 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